MacVector Changelog

What's new in MacVector 18.5

Nov 7, 2022
  • MacVector 18.5 adds a number of new functions, particularly regarding the identification of heterozygotes and mixed residues in ABI and Beckman chromatogram based Sanger sequencing data.

New in MacVector 18.2 (Oct 20, 2021)

  • MacVector 18.2 adds a number of new functions, particularly to the Align to Reference interface, along with a new Extra toolbar button that provides easy access to context-sensitive menu items in any particular tab.
  • Align to Reference Enhancements:
  • The Align to Reference alignment algorithm has been overhauled to do a much better job handling larger numbers of gaps in the alignment between a reference sequence and a read. Previously, for the standard alignment algorithm, more than 5 or 6 consecutive gaps in either reference or read would be poorly resolved. Now 20-40 consecutive gaps, such as might appear in CRISPR experiments are handled with ease, depending on settings. However, if you are expecting introns when aligning e.g. mRNA sequences versus a genome, you should still use the cDNA Alignment option which will also take splice site consensus sequences into account.
  • The alignment algorithm has been further optimized for speed and is now 2-10 fold faster depending on the sequences being aligned. In addition, the Sensitivity setting can now be lower due to the enhanced consecutive gap detection, which also speeds up calculations.
  • When aligning ABI chromatogram data, or plain sequences, the Map tab now graphically displays the “trimmed” regions at either end of the sequences making it far more obvious when there is only partial alignment between two sequences. This does not apply to NGS reads where it is impractical to view potentially millions of reads in the Map tab.
  • There is a new Remove Gaps context-sensitive (right-click) menu option that deletes residues in reads that correspond to a gap in the consensus sequence. This can clean up noisy assemblies where a low percentage of reads have extra residues inserted leading to a lot of gaps in the consensus sequence and a very cluttered display.
  • Context Sensitive "Hamburger" Menus:
  • Many of the views and windows in MacVector have context-sensitive menus available when you right-click (or -click) in them. To make the availability of these options more obvious, these views now contain an Extra “hamburger” button (three parallel horizontal lines);
  • Importing of Primer Databases in TSV or CSV Format:
  • You can now directly import primer data into a MacVector Primer Database (.nsub) file. First, prepare your data in an Excel or Numbers spreadsheet with three columns – “Name”, “Sequence”, “Comment”. Then export the data (or Save As...) in Tab Separated Values format or Comma Separated Values format. Open the file with TextEdit, select all the rows of text, Edit | Copy, switch to MacVector and select File | New From Clipboard. This functionality replaces the old Primer Converter utility which no longer runs on modern macOS systems.
  • Miscellaneous Enhancements:
  • To reduce clutter in the Assembly Project window toolbar, all of the assembly algorithms have been consolidated into a single Assemble toolbar button with a dropdown menu.
  • There have been a large number of minor enhancements to smooth out workflows and improve compatibility with the macOS and other applications. Some, such as reworking code behind the scenes to replace deprecated Apple functions and refactoring code for better stability and performance, help ensure that MacVector will continue to work on upcoming releases of macOS and take advantage of improved hardware.

New in MacVector 18.1.1 (Mar 8, 2021)

  • Universal Binary:
  • MacVector 18.1.1 is a Universal Binary, meaning that it can run natively on both Intel and Apple Silicon Macintosh computers. Other than the ability to run natively on M1 processors, MacVector 18.1.1 is essentially identical to MacVector 18.0.1 with the exception that the embedded Python framework has been updated to version 3.9. Currently, all of the embedded 3rd party algorithms are included as Universal Binaries with the exception of SPAdes and Bowtie – these run under Rosetta2 emulation on Apple Silicon machines. However, in our hands, they still out-perform equivalent older Intel- based computers.

New in MacVector 18.0.1 (Mar 8, 2021)

  • Cosmetic Changes for Big Sur:
  • The main application icon and window toolbar appearance have been updated to match the macOS Big Sur “look and feel”. MacVector 18.0.1 is still just an x86_64 “Intel” native binary, meaning that it runs under Rosetta2 emulation on Apple Silicon machines. There is a parallel MacVector 18.1.1 release that you should download if you are using an M1 machine and want to take advantage of a version of MacVector compiled to run natively on arm64 processors.
  • Improved Align to Reference SNP Reporting:
  • The align to reference algorithm has been slightly tweaked to do a better job of aligning reads that have insertions relative to the reference. The SNPa tab has been revised to use standard reporting for both nucleic acid SNPs and for corresponding changes to amino acid sequences in CDS features. In addition, small deletions are now reported, again using standard nomenclature.
  • Bug Fixes:
  • The use of a comma as the decimal point separator is now supported throughout MacVector for international localization.
  • Flye now assembles long read NGS data as expected.
  • A crash bug when “flipping” primer sequences in the Quicktest Primer interface has been resolved.
  • Using the Position Mask in multiple sequence alignments now works as documented.
  • Drag and drop is now disabled within an individual window as it could sometimes cause inadvertent corruption of the sequence.
  • Import of GFF files has been improved.
  • A crashing bug when extensively using the magnification function in the Map tab has been resolved.

New in MacVector 18.0.0 (Jan 5, 2021)

  • Overview:
  • MacVector 18 adds a number of new functions, including the ability to read a several requested file formats such as Sequencher assembly project files along with Serial Cloner and SnapGene sequence files. There is a new CRISPR PAM sequence searching function and a Trim by Quality option for Sanger sequence files. Finally, there are major enhancements to the protein multiple sequence alignment visualization of domains and the usual macOS compatibility enhancements. Note that while this release is not a native "Apple Silicon" build, it does work without problems on the latest M1 Apple processors and a new MacVector 18.1 release with full Apple Silicon Universal Binary support is just around the corner.
  • Searching for CRISPR PAM Sites:
  • There is a new feature accessed by the Analyze | CRISPR PAM sites... menu item that will scan Nucleic Acid sequences for Protospacer Adjacent Motifs associated with the CRISPR Cas9 and related enzymes cleavage and modification functions. By default, MacVector uses a file called Protospacer Adjacent Motifs.pam that is located in the /Applications/MacVector/Subsequences/ folder. It contains most of the current Dec 2020) characterized Cas9-like enzymes, but you can always open the file and add your own. While MacVector does not currently search genomes for potential off-target sites, this is still a very useful function to alert you to potential CRISPR target sites. The output is a mix between the current Restriction Enzyme and Nucleic Acid Subsequence searches, so you can easily see and copy the guide sequences. You can also have MacVector automatically scan for CRISPR PAM sites whenever you open a DNA sequence file - control this using the MacVector | Preferences | Scan DNA pane.
  • The results are shown in the Map tab, and you can zoom in to see the actual sequence of the hits with the guide sequence shown in lower case and the PAM sequence in upper case;
  • Support for Additional File Formats:
  • You can now import SnapGene .dna files, complete with feature colors, like this plasmid downloaded from the AddGene website;
  • Or .spf Assembly Project files from Sequencher;
  • In addition, you can now import .xdna files from Serial Cloner, which is an extended version of the old DNAStrider format.
  • Enhancements to Outlining Shared Domains in Aligned Sequences:
  • First added in MacVector 17.5, this functionality has been significantly enhanced to expose additional Feature-related functionality in Multiple Sequence Alignment documents. There is a new Features tab in the protein multiple sequence alignment window where you can view, edit, create and/or delete features in each of the aligned sequences.
  • When the Editor or Picture tabs are active, a new floating Graphics Palette is displayed (similar in concept to the Graphics Palette for the single sequence Map tab), allowing you to turn features on and off permitting greater control over how shared domains are displayed and outlined.
  • Trim by Quality:
  • Both the Align to Reference and Assembly Project windows now let you trim reads based on quality. The reads (typically Sanger sequencing reads in ABI or SCF format) should not be aligned prior to running the algorithm. A typical workflow might thus be to add .ab1 or .scf files to a project, optionally base call with phred, if needed, then Trim by Quality prior to aligning or assembling.
  • Miscellaneous Enhancements:
  • There have been a large number of minor enhancements to smooth out workflows and improve compatibility with the macOS and other applications. Some, such as reworking code behind the scenes to replace deprecated Apple functions and refactoring code for better stability and performance, help ensure that MacVector will continue to work on upcoming releases of macOS and take advantage of improved hardware. In particular, MacVector 18 now includes embeded versions of Python and Perl as recommended by Apple to future-proof the application against changes to the macOS.

New in MacVector 17.5.0 (Feb 10, 2020)

  • Outlining Shared Domains in Aligned Sequences:
  • Multiple Sequence Alignments now retain feature information from their individual input sequences and can use this information to outline shared domains in the aligned sequences. To use this feature, first individually annotate the sequences you want to align, make sure the domains/features you are interested in are visible and set the Fill color to the color you would like to see in the alignment. Then add the sequences to a multiple sequence alignment document and align in the usual way (or, keep the single sequence documents open and choose Analyze | Align Multiple Sequences Using...). Then click on the Mode toolbar button (shown below) and select Show Features.
  • This turns on a simple feature display mode in the Editor tab where you can see the extent and color of the features. When you switch to the Picture tab, you will see colored outlines around the shared domains;
  • Flye is an assembler algorithm tuned to assemble poor quality long reads such as those produced by PacBio and Oxford Nanopore sequencers. Because these reads tend to be very error prone, MacVector 17.5 also includes an optional polishing step using Racon. With typical bacterial genome assemblies, it is fairly common to be able to assemble reads into a single full-length genome contig, such as with this set of reads from a strain of E. coli;
  • Note that it is important to tell MacVector what type of reads you are assembling - this is easily done by double-clicking on the Status item after importing the reads via the Add Reads toolbar button.
  • The three jobs above are the result of varying Flye parameters. However, all three resulted in a single contig approximately matching the size of the E. coli genome - the differences in length reflect different "polishing" strategies with the last one having one round of internal polishing by Flye and one additional round of polishing by Racon.
  • As one of the last steps in Flye assembly, MacVector aligns the input reads against each contig consensus using minimap2 so that you can view the alignments in the Contig Editor. Because of the noisy nature of Long Read sequence data, MacVector removes additional erroneous inserted residues in each read prior to display to clean up the visual alignments.
  • Contig and Align to Reference Editor Enhancements:
  • There have been a number of enhancements to these editors, primarily to aid in visualizing edits and quality values and to "clean up" the visual appearance of alignments.
  • Residue Background Colored by Quality:
  • A Shading toolbar button lets you turn on coloring based on the quality value assigned to each residue;
  • The intensity of the colors indicates the phred-based quality value of each residue. For individual reads, this ranges from 0 (deep red) through 20 (white) to 40 or above (deep green). The consensus scale is doubled and ranges from 0 (deep red) through 40 (white) to 80 or above (deep green). Gaps are always shown with a white background. As with earlier versions of MacVector, you can "mouse-over" a residue to view the numerical information in a tooltip.
  • Edited Residues Have a Blue Background:
  • Edited residues are always given a phred quality value of 99 - these residues are given a blue background;
  • Base Calling with Phred:
  • You can now directly run phred on Sanger sequencing trace files in the Align to Reference Editor by clicking on the Basecall toolbar item with the appropriate sequences selected;
  • Note that you must do this before aligning the sequences. You can always "reset" (i.e. un- align) and sequence by selecting its name and choosing Reset (un-align) Selected Reads from the right-click (or -click) context-sensitive menu.
  • Editing Enhancements:
  • There are some new context-sensitive menu items in the Align to Reference Editor tab
  • Delete Clipped Residues - deletes any greyed-out ("clipped" or "trimmed") residues. While these are ignored by the consensus calculation, some users prefer to delete them for a cleaner looking alignment.
  • Close Gaps by Deleting Residues - you'll often see gaps in the consensus where one or more reads has an additional erroneous inserted residue. This menu item removes the extra residues from the read, cleaning up the visual appearance of the alignment.
  • You can now "nudge" reads in the Align to Reference Editor tab. Select the name of the sequence you want to nudge and use the left/right arrow keys to move it around. If you have problematic alignments where you need to physically insert residues or gaps, hold down the key when typing to insert the residue or gap before the currently selected residue, then use the nudge function to get the alignment right. The consensus updates in real time.
  • Miscellaneous Enhancements:
  • There have been a large number of minor enhancements. Some, such as reworking code behind the scenes to replace deprecated Apple functions and refactoring code for better stability and performance to help ensure that MacVector will continue to work on upcoming releases of macOS and take advantage of improved hardware. There have also been improvements to Dark Mode support in many areas and much better handling of the labels in crowded Map views.

New in MacVector 17.0.8 (Nov 1, 2019)

  • macOS 10.15 “Catalina” Compatibility:
  • A glitch in the Analyze | Primer Design/Test (pairs) dialog has been resolved where the advanced parameters either could not be viewed or were displayed in a garbled form.
  • A crash double-clicking on a feature item in the floating Graphics Palette window has been fixed.

New in MacVector 17.0.7 (Nov 1, 2019)

  • Bug Fixes and Enhancements:
  • Toolbar buttons are now correctly enabled/disabled in the Restriction Enzyme window. The Primer Design/Test (pairs) function no longer gets in an invalid state under certain
  • circumstances when a hybridization primer is not specified.

New in MacVector 17.0.6 (Nov 1, 2019)

  • Bug Fixes and Enhancements:
  • You can now use File | Export to export all contig consensus sequences from an Assembly Project (e.g. after a SPAdes assembly) in a fastq file. Previously this only worked for fasta exports.
  • You can now “slide” reads in the Contig and Align to Reference Editors. This is only functional for simple “memory-based” assemblies in the Contig Editor, not the NGS assemblies that use a read-only BAM file as the backing store.
  • You can now dissolve individual contigs in phrap job results. Again, this is only for “memory-based” assemblies such as ABI or plain sequence files, not NGS-based data.
  • A bug where features would get duplicated when overwriting a sequence by pasting has been fixed.

New in MacVector 17.0.5 (May 17, 2019)

  • Bug Fixes:
  • A problem connecting to network KeyServers due to the “code-hardening”we had to add to support notarizing has now been resolved. A crash when editing certain LOCUS lines has been fixed.
  • Another “code hardening” issue with importing BAM files into the Assembly Project interface has been fixed.

New in MacVector 17.0.2 (Mar 4, 2019)

  • Bug Fixes:
  • Multi-segmented CDS features are now correctly translated in text output windows.Segmented alignments are now correctly displayed in the Align to Reference Map tab.
  • The Base Composition text output now correctly calculates the“T”composition.We have found a workaround for problems printing many graphical image views under macOS Mojave.

New in MacVector 17.0.1 (Feb 18, 2019)

  • Bug Fixes:
  • The cDNA Alignment algorithm in the Align to Reference function now generates results similar to MacVector 16.
  • A crash when hovering the mouse pointer over a tab bar with the key held down has been fixed.
  • A problem opening saved Gibson Assembly projects on macOS versions prior to 10.14 has been resolved.
  • A variety of issues editing and selecting sequences in the Multiple Sequence Alignment Editor have been fixed.
  • When you select and ORF in the Open Reading Frame analysis results window, the corresponding region in the parental sequence is now selected.

New in MacVector 17.0.27 (Feb 7, 2019)

  • Dark Mode Support:
  • MacVector 17 has basic support for the macOS Mojave “Dark Mode”. Many of the icons have been reworked and the background and foreground colors and the tab bars of most windows are now dynamic so that text and graphics are clear and legible under both Dark and Light modes.
  • Restriction Enzyme Picker:
  • There is a new floating window that displays a list of Restriction Enzymes that cut the currently active sequence, even if those enzymes are not currently visible in the Maptab.
  • The entire interface is interactive, so you can move the sliders to filter by number of cuts or site size, or choose the end structure (5’ overhang, 3’ overhang, blunt) or toggle individual enzymes on and off. You can save any set of enzymes in a separate filefor use in Analyze | Restriction Enzymes...analysis. You can show/hide the window when you are not interested in restriction enzymes using the RE Pickertoolbar button(note there is also now a companion button to show/hide the Graphics Palette)
  • Gibson/Ligase Independent Cloning:
  • There is a completely new interface and document type to handle a variety of ligase-
  • independent cloning strategies. The interface supports both the 5’ exonuclease driven “Gibson” assembly technique as well as the T4 DNA Polymerase 3’ exonuclease “Ligase Independent Cloning” approach. You can have MacVector automatically design primers for you, or you can provide custom primers you have designed yourself manually, or with popular internet tools such as the NEBuilder website. You can also just provide existing fragments with overlapping ends for MacVector to assemble. The interface also shows the exact structure of the junctions between fragments, including relevant CDS translations so that you can check you have protein fusions in the correct frame.
  • The interface is highly interactive –you can drag features into it from other sequence documents and even drag a restrictionenzyme(s) into it from a vector to use the cut vector as a base for you cloning experiment. The recommended primers are listed in a separate tab that can be printed or copied to other applications, so you can document them before sending them off for synthesis. A simple click creates the new circular molecule once all ends have been accounted for. The entire project can be saved as a new document type, and any fragment can be separately opened in a normal sequence window either before or after applying PCR primers.
  • Genome Comparison:
  • In recent years that has been an explosion of whole-genome sequencing projects. One common question coming out of this has been to ask“Exactly what are the genetic differences between my sequenced organism and another related strain?” MacVector to the rescue! A new Analyze | Compare Genomes By Feature...featurelets you see the differences between two annotated genomes in fine detail. The function takes every annotated feature from the source genome and looks for the presence of that feature in the comparison genome based on sequence similarity. CDS features are even translated so that the predicted amino acid sequences are compared. The results are then tabulated to show identical, closely related, and weakly related features in separate tabs, with additional tabs for features that are completely missing and a “details” tab that shows the low-level alignment details for any matching pair of features. Hot-links in the result tabs let you quickly scroll the parent sequences to any individual feature of interest.
  • Assembly Jobs:
  • You can now run multiple jobs in an assembly project and each job is encapsulated in its own job object in the Assembly Project window.This gives you much greater flexibility in organizing your assembly tasks and each job is given an intuitive name.
  • There is a properties tab that lists all of the relevant details for the currently selected job, including input parameters, total assembled reads, average contig length, total contig length and even N50 to give you an idea of the quality of genome assemblies. A popup menu lets you quickly switch between different jobs.
  • Coverage Tab:
  • Assembly projects now have a Coveragereport that allows you to select a reference sequence and directly compare multiple reference assemblies. You can compare different sequencing datasets assembled against the same reference sequence with expression level comparison.Now that you can store multiple assembly jobs in a single Assembly Project, then you can also directly compare multiple runs of the same dataset against a single reference sequence to compare which is the best assembly.
  • Assembly Problems:
  • Align to Referencenow has a Problemstabthat helps you identify mis-assembled genomic sequences based on excessive mismatches, discontinuous reads and other common problems.The primary aim of this tab is to help you identify potential assembly issues with genomic sequencing projects. You can use Align to Reference to assemble several million reads against a typical small genome (practically, up to ~10 Mbp or so) and the tab will report those regions that are most likely to be misassembled.
  • Scan for Primers:
  • MacVector now automatically scans DNAsequences for primerbinding sites whenever you open a DNA sequence, in addition to the RestrictionEnzymes, Open Reading Frames and Missing Features introduced in previous versions. By default, the collection of primersin the /MacVector/Subsequences/PrimerDatabase.nsubfileare used, but you can use any .nsubfile you like, configured using the updated MacVector|Preferences|Scan DNA preference settings
  • Use of APIKeys with Entrez and BLAST:
  • The NCBI have introduced a new system for accessing the Entrezdatabase over the internet. They now throttle general accesses to the Entrez server to no more than 3 calls per second per IP address. This might seem a lot, but if you want to download a list of 100 sequences, this can really slow things down, especiallyif you are sharing a public IP address behind a company or university firewall and others are using MacVector. They have introduced a new “APIKey” concept –you can request one of these from the NCBI for your own personal use and that increases the permitted rate to 10 calls per second and is independent of the IPaddress. Thus, you can share a public IP address with colleagues and still each have the full 10 calls per second access.
  • How Do I:
  • There’s a brand new How Do I menu that shows common workflows with simple step by step guides and short videos. Every tool dialog now has direct access to a simple video/tutorial on how to use it.
  • Miscellaneous Enhancements:
  • You can now copy and paste features between sequence documents. Simply select the feature in the Features tab of one sequence, Edit | Copy, then switch to another sequence Features tab and choose Edit | Paste.
  • You can now select a short sequence in a Read in the Align ToReference Editortab, right-click to bring up a context sensitive menu, and then select all of the other aligned reads that contain that a sequence. It’s a great way of selecting all the reads with a specific SNP(s). Combine it with selecting the pairs for each read with NGS data and saving the selected reads and you have a very powerful way of analyzing SNPs or resolving repeat sequences in genomic assemblies.
  • Some of the nomenclature and interactions in the Primer3 dialog box have been cleaned up to simplify its use.
  • You can now add sequences to the Align To Referencewindow from multi-sequence GenBank files
  • GenBank multi-sequence files now open by default as individual sequences.
  • When results are generated for the Bowtie Coveragetab, the name of each feature is now displayed exactly as per the label used in the Maptab allowing you more control over exactly how the text appears.
  • There is now an option in the Database| Auto-annotate Sequence...interface to automatically “fix” CDS features. This will change the stop location if the match creates a longer or shorter open reading frame and will also change the contents of any /translation= qualifier to reflect the new translated coding sequence.
  • The Align to Referencealgorithmis nowmulti-threaded. You will see a significant speed up, particularly if you are using larger Sensitivityvalues, though we still recommend keeping Sensitivityto a low (

New in MacVector 16.0.8.33 (Jan 31, 2018)

  • Bug Fixes:
  • The NCBI changed the behavior of the Entrez server for retrieving sequences in the BLAST hit list. This release has some changes to restore that functionality.

New in MacVector 16.0.7.32 (Jan 29, 2018)

  • Bug Fixes:
  • The ability to copy Feature information from the Features tab has been restored. MacVector no longer hangs when analyzing Protein sequences with over 32,000 residues.
  • MacVector now does a better job of opening multiple sequence alignment files with internally corrupted Newick guide trees.
  • There have been additional changes to improve the stability of large Align To Reference alignment jobs.

New in MacVector 16.0.6.31 (Jan 18, 2018)

  • Bug Fixes:
  • Some minor issues with Align To Reference when reads aligned starting at the last residue of circular sequences has been fixed.
  • MacVector now does a better job of parsing malformed Genbank LOCUS lines.

New in MacVector 16.0.5.29 (Dec 21, 2017)

  • Bug Fixes:
  • A crash when editing names in the MSA Editor with fewer than 4 sequences in the alignment has been fixed.
  • There have been some changes to the threading of Align To Reference jobs to help prevent occasional crashes on certain machine/OS combinations.
  • New features once again honor the settings in the default Symbol Editor. This was
  • inadvertently broken in MacVector 16.0.3.

New in MacVector 16.0.3.27 (Nov 17, 2017)

  • Bug Fixes:
  • An occasional crash when rapidly moving the mouse pointer around the Quicktest Primer dialog has been fixed.
  • A problem recalculating phylogenetic trees has been fixed.
  • You can now select multiple features in the Map view, double-click on one and the multiple-Symbol Editor will be displayed.
  • Using the Free-form Feature Editor tab no longer deletes qualifiers.
  • All of the controls in the MSA Editor Preferences are now wired up correctly. Some extraneous asterisks in the MSA text output have been removed.

New in MacVector 16.0.2.24 (Nov 9, 2017)

  • Bug Fixes
  • A crash when invoking the Align to Reference Add Seqs function on OS X 10.7 and OS X 10.8 has been fixed.
  • When you Export a sequence in GenBank format, MacVector now writes out all GenBank features, even if they are currently obsolete.

New in MacVector 16.0.1.23 (Nov 9, 2017)

  • Bug Fixes:
  • A critical bug where MacVector crashed when unlocking a document after invoking Options | Symbols For Xxx... has been fixed.

New in MacVector 16.0.0.20 (Nov 3, 2017)

  • Enhanced automatic sequence annotation, a simplified combined Feature/Symbol Editor, a new Assembler algorithm (SPAdes) and lots of other improvements.
  • Scan For Missing Features:
  • Whenever you open a DNA sequence, MacVector now scans it to identify common features that are not already annotated on the sequence. Its shows these in faded colors in the Map tab so that you can see what features are missing from your sequence. By default, MacVector uses the collection of features in the /MacVector/Common Vectors/Annotated Fragments/ folder, but you can use any folder you like, configured using the new MacVector | Preferences | Scan DNA preference settings.
  • You can right-click on any faded feature to add it to your sequence, or select all of them and add with a single mouse-click.
  • Combined Feature/Symbol Editor:
  • If you double-click on an individual feature in the Map tab, it now brings up a dialog with two tabs – one for the Feature Editor and one for the Symbol Editor. This lets you edit both the basic Genbank-style feature information and the graphical symbol appearance in a single dialog. Note: this is only displayed when you are editing a single individual feature. If you want to change the appearance of multiple features at the same time, you will get the normal Symbol Editor.
  • Assembler Improvements:
  • We have added the popular SPAdes algorithm to Assembler for MacVector 16.0. This is a high-performance assembler that uses very little RAM, allowing it to run on relatively modest machines, though we do recommend 16GB+ of RAM for optimal performance. It is a little slower than our existing velvet algorithm, but does a better job of resolving repeats at the ends of contigs, so you generally find it produces longer contigs with the same input data. One drawback of SPAdes is that it does not generate alignments, only contig consensus sequences, so we have added an option to generate alignments within MacVector using bowtie. This does increase processing time.
  • You can now use interleaved paired read files for all NGS assembly algorithms (velvet, bowtie and SPAdes). MacVector will automatically identify them where possible.
  • MacVector now directly supports compressed fasta and fastq formatted files (.zip or .gzip) and will submit those directly to assembly algorithms. This dramatically reduces the amount of temporary disk space required when assembling large datasets.
  • There are now more options to control the type of read that you are using (unpaired, paired-end, mate pair, HQ mate pair, NxSeq long mate pair), or the source of the reads (Illumina, IonTorrent, PacBio, Nanopore etc). Double-click on a read after importing into a project to set these parameters. SPAdes in particular will optimize assembly based on these settings.
  • There is now a right-click option to circularize contigs in the Contig Editor. If there are direct repeats at the ends of a contig, you can right-click and the item will show you the length of the repeat. If you select the item, a new circular sequence will be created from the consensus.
  • Miscellaneous Enhancements:
  • In the single nucleic acid sequence editor view, when you hover the pointer over a residue, the tooltip now displays the nucleic acid residue number under the pointer, and also the amino acid residue number of any annotated CDS feature at that position.
  • The Align To Reference assembly algorithm has been improved to better handle reads crossing the circular origin of a reference sequence. It is also now significantly faster when aligning longer reads with multiple regions of mismatches.
  • Multiple Sequence Alignments now have an option to “unalign” selected sequences, or the entire alignment – it’s an option on the Align toolbar button.
  • By default, MacVector now uses a smaller arrow for ORF results, with a pale red color for matches on the plus strand and pale grey for matches on the minus strand to distinguish them from annotated features.
  • MacVector 16 has had yet more functions added to the AppleScript directory. To see what functions are available, open the apple-supplied Script Editor, choose File | Open Dictionary and select the MacVector.app application. For examples of using AppleScript to drive MacVector, see sample files in the /Applications/MacVector/AppleScripts/ folder.
  • Bug Fixes:
  • Find Sequencing Primers/Probes now honors the % GC and Tm limits.
  • Some parameters in the Analyze | Primer Design/Test (pairs) “Test Primer Pair” function
  • which were previously hidden have now been revealed.
  • The Analyze | Base Composition algorithm now generates the correct Tm data for very short window sizes.

New in MacVector 15.5.4.38 (Oct 3, 2017)

  • Automatic Updater:
  • This release adds additional functionality to the online updater code to simplify updating to the forthcoming MacVector 16.0 release.

New in MacVector 15.5.3.35 (Jul 1, 2017)

  • Bug Fixes:
  • A bug where the number “0” would sometimes appear in the wrong place on the numbering line of a Map tab has been fixed.
  • The settings for the automatic ORF calculation and display have been tweaked to allow better control over large sequences. A bug where the automatic RE limit was ignored has also been fixed.

New in MacVector 15.5.2.33 (Jun 10, 2017)

  • Bug Fixes and Enhancements:
  • The Primer Design/Test Primer Pairs... function now correctly honors the “Max mismatches” parameter.
  • A minor tweak to the Bowtie functionality now prevents matching “dovetailed” reads from being written to the unaligned reads files. “Dovetailed” reads are those where due to a small insert size the mate pair sequences extend beyond the beginning of their mate.

New in MacVector 15.5.1.32 (Jun 1, 2017)

  • Bug Fixes and Enhancements
  • MacVector now alerts you if the license you are using has been updated. This lets you
  • know that your lab or Institution has extended the maintenance period to ensure that you
  • are entitled to new versions as we release them. The auto-ORF display now uses the same length limit as the auto-Restriction Enzyme display so that they are not unnecessarily calculated for long sequences.
  • A crash when closing certain Multiple Sequence Alignment documents has been fixed.
  • A few issues with the display of alignments resulting from phrap assemblies have been
  • resolved.
  • You can now Reverse and Complement a chromatogram file in the Trace Editor and the
  • sequence does not get inappropriately greyed out.
  • An issue where pasting a fragment in the “flipped” orientation would occasional crash
  • has been resolved.
  • An issue where pasting flipped fragments would occasionally corrupt features that
  • crossed the ends of the fragment has been fixed.
  • The cloning clipboard now correctly handles digestion of a linear sequence to create two fragments with one blunt end (e.g. from a PCR experiment) and one restriction generated
  • end.
  • A problem editing MSA alignments in NA + virtualAA mode has been fixed.

New in MacVector 15.5.0.31 (May 8, 2017)

  • Graphical DNA BLAST Results:
  • There is a new graphical BLAST results tab. It displays a graphical alignment of the query sequence aligned against each high scoring segment pair of the BLAST hits (NOTE: individual hits may have multiple high scoring segment pairs). This allows you to clearly see which genes or features your query is aligning to. If there are too many features to display in the graphical pane, simply hovering over it will expand to display all overlapping features. For each hit, you can choose to download the entire sequence, or, particularly useful for hits to entire genomes, just the aligned segment plus ~2kb either side.
  • This interface represents a new and powerful approach to quickly identifying the function of your query sequence. With the advent of NGS genomic sequencing, any bacterial query sequences in particular typically match entire genomes – this allows you to identify and download just the region that matches your sample sequence for further detailed analysis within MacVector.
  • Automatic ORF Display:
  • MacVector now automatically searches for open reading frames in every DNA sequence that you open. This works similarly to the existing automatic Restriction Enzyme display. There is a new DNA Map tab in the main Preferences window that controls both of these functions;
  • Note that there is a checkbox (turned on by default) to suppress the display of ORFs that are already annotated on the sequence. In addition, the default appearance of ORFs has been changed to be less obtrusive in crowded Maps and they are now labeled with the length of the ORF;
  • Align to Reference Editor Context Menu:
  • Both the Align To Reference Editor and Contig Editor now have context sensitive menus. To invoke these, simply right-click (or -click) in the window. Many of these functions have been specifically designed to simplify the use of MacVector for closing the gaps in bacterial genome sequencing projects. The functions available for the Align To Reference Editor are;
  • Export Consensus with/without Gaps Align Selected Reads
  • Delete Selected Reads
  • Reset (unalign) Selected Reads
  • Export Selected Reads as FASTA/FASTQ Select Matching Pairs (*)
  • Extend Reference with Selected Read (**)
  • (*) – if you have aligned a set of paired-end reads, you can select individual read(s) and use this function to select the corresponding mate(s). This is particularly useful if you want to find pairs that will extend a contig and export them for further analysis/assembly.
  • (**) This is active if you have selected a single read that hangs over either end of a Reference sequence. This will extend the Reference in the appropriate direction using the sequence of the read.
  • The Contig Editor has a subset of these functions with just the Export... and Select Matching Pairs functions available.
  • Miscellaneous Enhancements:
  • Map windows now update when you change the default appearance of features.
  • A number of menu items have been renamed to more clearly explain what they do. ORF results can now be filtered by minimum length.
  • Some bugs saving large assemblies have been fixed.
  • A number of issues selecting different display options in the Phylogenetic
  • Reconstruction tree display have been resolved.
  • A few intermittent crashes when editing Multiple Sequence Alignment documents have
  • been fixed.
  • MacVector now does a better job of interpreting complicated Bowtie alignments so that the alignment display has fewer out-of phase mismatches, whilst still retaining all of the residues in each read.
  • There is now an option to control the length of vertically oriented labels in the Map tab. A bug where you could not display multiple digest when just a small number of
  • restriction enzymes were used has been resolved.
  • By default, only the main three NCBI databases are now shown in Entrez searches. You can ask to view more, but you may not be able to retrieve sequences from many of the others, other than through a browser.
  • A number of default settings have been changed to enhance the interface experience for new users.

New in MacVector 15.1.5.25 (Feb 14, 2017)

  • Bug Fixes:
  • The Restriction Enzyme double-digest output now works as expected when just two or three enzymes are selected.

New in MacVector 15.1.4.24 (Jan 10, 2017)

  • Bug Fixes:
  • The 3/6 frame translation in the single sequence editor now correctly maintains the frame after a line wrap.
  • A crash when turning on 3/6 frame translation in the Align To Reference Editor with a sequence larger than 65,000 residues has been fixed.

New in MacVector 15.1.3.23 (Dec 16, 2016)

  • Bug Fixes:
  • A bug in the Multiple Sequence Alignment Editor has been fixed.
  • The effect of this bug was that additional residues sometimes appeared at the beginning of sequences when they were saved.
  • This only affected MSA documents that were edited.
  • If you just aligned with ClustalW/Muscle/T-Coffee and saved without editing, the alignments would be correct.

New in MacVector 15.1.2.22 (Dec 2, 2016)

  • Bug fixes:
  • Occasionally, filling in ends in the Cloning Clipboard ligation dialog did not always result in the correct sequence being added to the resulting molecule. This bug has been fixed in MacVector 15.1.2.

New in MacVector 15.1.1.21 (Nov 3, 2016)

  • Bug fixes:
  • Crashes when saving certain edited Multiple Sequence Alignment (.msan, .msap) documents have been resolved.
  • A bug where some fastq reads would be written out multiple times from the results of an Align To Folder search has been fixed.
  • The Align To Reference SNP tab now reports indels in the consensus report section as well as SNPs.
  • You can now delete gaps in the Align To Reference Editor. As always, to insert a residue, hold own the key.
  • You can now -click to select extended sections of Read sequences in the Align To Reference Editor.

New in MacVector 15.1.0.17 (Oct 28, 2016)

  • NCBI Online BLAST and Entrez:
  • The US Government has required that all government-run internet services must switch to the more secure https: protocol by the end of 2016. The NCBI provided a new https: service for BLAST and Entrez starting Sept 1st 2016. The MacVector BLAST and Entrez functions have been completely rewritten “under the hood” to use the new services.
  • At the time of writing, it is anticipated that the BLAST and Entrez functions of all earlier versions of MacVector (up to and including 15.0.3) will cease to work on or about Dec 1st 2016. All users who wish to continue using BLAST and Entrez within MacVector should upgrade to MacVector 15.1 prior to this date to ensure uninterrupted service.
  • Miscellaneous Enhancements:
  • The Velvet assembler can now use KMER values up to 299 (previously it was limited to 99). If you are assembling genomic MiSeq NGS data, try setting KMER to values in the 221 to 281 range to get optimal alignments.

New in MacVector 15.0.3.34 (Sep 9, 2016)

  • Bug fixes:
  • A glitch in the Multiple Sequence Alignment (MSA) Editor where it was possible to delete residues while sliding a block of text around has been fixed.
  • Opening Fasta formatted files containing protein sequences now always opens the files as amino acid alignments.
  • A display problem where residues might get clipped at the right side of the Single Sequence Editor has been fixed.
  • Missing “dashes” in the MSA Picture tab have been fixed.
  • Copying RNA sequences from the MSA Editor now correctly retains the U’s rather than
  • converting them to T’s.
  • When using the MSA Editor in DNA+virtualAA mode, selecting and copying the translated amino acid sequences now places protein residue information on the clipboard.
  • When zoomed to the residue level in the Map results tab, multi-part subsequence search hits now display the correct sequence for the second and subsequence parts.

New in MacVector 15.0.2.32 (Aug 23, 2016)

  • Enhancements:
  • The range popup menu now displays the same text that is used as the label in the Map tab.
  • Copied sequences containing CDS features now preserve the original frame via adding a /codon_start qualifier.
  • The mono-spaced text output now uses the same label text as the Map tab.
  • There are new “thin” versions of the Hollow Box and Hollow Arrow graphics symbols.
  • The Multiple Sequence Alignment Editor tab now supports File->Export Tab Contents As...
  • You can now use the Edit | Transformations | Maker lower case/Make upper case menu items in the Subsequence/Primer editor.
  • Bug Fixes:
  • Sometimes the SNP tab in the Align To Reference window would show “no text”. This
  • has been fixed and the SNP text data has been enhanced to include additional information.
  • The selected Genetic Code is now honored in all views containing translations.

New in MacVector 15.0.1.28 (Aug 10, 2016)

  • CRISPR Indel Detection:
  • There is a new preset in the Align To Reference alignment dialog that optimizes the parameters for use in CRISPR indel detection at the cost of slower performance. These settings are tuned to allow for insertions of up to 10 nt in length and deletions of any length. In addition, the alignment algorithm has been adjusted to generate much cleaner alignments across the indel locus.
  • Bug Fixes:
  • An intermittent problem that affected a subset of users in many different ways running OS X 10.10 (“Yosemite”) has been resolved. These included inability to open certain file types and even crashes on startup.
  • Fasta files can now be correctly imported via the file system or by the File->New From Clipboard interface.
  • The ability to enter ambiguous residues in the Align To Reference/Contig Editor has been restored.

New in MacVector 15.0.24 (Jul 19, 2016)

  • InterProScan:
  • You can now scan proteins for functional domains using the popular online InterProScan collection of algorithms. This is accessed from the Database menu. You can easily permanently add the found domains as features by clicking on the little plus icons next to the graphic representing each domain.
  • Multiple Sequence Alignment Enhancements:
  • There is a new Mode toolbar button in the Editor tab of both protein and DNA multiple alignments. For proteins, this lets you assign the last sequence as a “reference” so that the displays key off that sequence when showing similarities. This allows you to view proteins in a similar way to the DNA Align To Reference interface.
  • The second new capability is that you can now view and align DNA sequences via their virtual translations. You can choose to display both the DNA sequences and their amino acid translations at the same time (or even just the amino acid translations). When amino acids are displayed, you can use ClustalW, Muscle or T-Coffee to align the amino acid translations – the alignments are then reflected in the underlying DNA sequences. Everything is updated dynamically as you edit so that you can delete DNA residues and immediately see the impact of the change on the amino acid alignments.
  • Miscellaneous Enhancements:
  • The Database | Auto-annotate Sequence function now supports Applescripting. There is an example script in the /Applications/MacVector/Applescripts folder. You can create a misc_feature by right-clicking on any restriction site to have a permanent record of any RE site associated with the sequence.
  • There have been a number of tweaks to the Map view to clean up the display e.g. better positioning of graphics to avoid even minor overlap between them at high resolution and better handling of labels to reduce the amount of text displayed.
  • A new option to control the size of font in lists and tables. You can now undo CluatalW/Muscale/T-Coffee alignments.
  • You can now choose the /regulatory_class of a Regulatory elements from a popup menu. The Regulatory type replaced the old -10, -35, enhancer etc types in the last couple of years in the Genbank standard.
  • Termination codons (“*”) are now retained after alignment by ClustalW/Muscle/T- Coffee rather than getting converted to X.
  • The Primer Database editor now directly supports entering “tails” as lower case residues.

New in MacVector 14.5.3 (Apr 20, 2016)

  • Bug Fixes:
  • An occasional crash in the Align To Folder function has been fixed.
  • A rare crash when testing pairs of primers has been fixed.

New in MacVector 14.5.2 (Feb 21, 2016)

  • Bug Fixes:
  • Align To Folder now correctly handles searches using a segment of a sequence that crosses the circular origin.
  • Turning “Automatic RE Searching” on/off in the Map Preferences now correctly updates all open windows.

New in MacVector 14.5.1 (Jan 26, 2016)

  • Bug Fixes:
  • When you try to enter out of range values in sequence analysis dialogs, the error messages are now more informative.
  • You can now correctly export Genbank files containing the “between” location identifier (e.g. 123^124) and the Map tab now correctly displays the exact location for all feature appearance types.
  • The “Segmented Hollow Arrow” feature appearance type now draws correctly for features on the complementary strand.
  • An extra residue was getting included when copying the product of a Primer3 amplification – this has been removed.
  • Users can now override the file extension when exporting in a different format (e.g. you can now export Genbank files with a .txt extension).
  • You can now Export Tab Contents As agarose gel images in formats other than PDF.
  • Agarose Gel images now print correctly in black-bands-on-a-white-background mode.
  • The Align To Reference Editor has had some work to clear up some hangs and allow more consistent editing behavior when attempting to modify the reference sequence.
  • Some problems when trying to linearized plasmids by selecting a restriction enzyme and clicking on Digest have been resolved.
  • Filtering Restriction Enzyme Search results using “End Structure” now works as expected.

New in MacVector 14.5.0 (Jan 2, 2016)

  • Simulated Agarose Gels:
  • By far the coolest new feature is a completely new interactive interface that lets you preview lifelike images of agarose gels. You create an agarose gel window by choosing File | New | Agarose Gel and then simply drag restriction enzymes from and Map views and onto the Agarose Gel window to view the banding patterns.
  • There are settings to control the percentage of agarose in the gel, the length of time the gel is run for, the level of graphical realism, the approximate position of marker dyes and the display of band sizes superimposed on the gel.
  • We include a collection of common DNA size markers that you can easily add to the gels, but you can also create your own with a simple text editor.
  • All gels can be saved to disk and printed in white on black or, to save ink, black on white formats.
  • Miscellaneous Enhancements:
  • The Align To Reference editor has been rewritten to allow the import and alignment of much larger fastq files containing NGS reads. It is now practical to import 20 million+ reads into the document and align them reasonably quickly – 20 million 50nt reads will align against a 2kb reference in less than 5 minutes with the appropriate settings.
  • You can now run Align To Folder searches against paired-end Fastq or Fasta formatted NGS data files. When you subsequently retrieve matching reads from the Description List, both reads of a pair will be retrieved into a pair of “hit” files. This dramatically simplifies e.g. “cloning” of genes from RNASeq data or finding reads to extend the ends of a contig.
  • The Graphics Palette now contains a control displaying the current magnification factor and a stepper control allowing you to easily increase or decrease the radius of circular vectors.
  • You can now jump to alphabetically listed RE sites in the Results section of the Graphics Palette by typing the first letter of the name of the enzyme.
  • There is a new Edit | Remove Gaps function to remove gaps in single sequences and also in the Align To Reference and Contig editors.
  • The contents of the Cloning Clipboard can now be copied as a graphical PDF object – great for creating drawings in e.g. Adobe Illustrator outlining the derivation of a construct.
  • There are new Options | Fonts | Bigger/Smaller menu items that change the font sizes in most text-based windows. These include the Editor tabs, all of the plain text output windows and no also the table-based views (e.g. the Features and Annotations tabs). You can use -“minus” and -“plus” as shortcuts. Note you need to hold down the key to type “plus” as -“equals” re-runs the last used analysis function.
  • The “Frame” option has been restored to the sequence Find function. This is particularly useful if you are looking for the location of specific codons in a coding region.
  • The Map tab has been reworked so that you can now zoom into a smaller region of a sequence without losing any existing selections.
  • MacVector 14 Limitations on Mac OS X 10.6:
  • In order to take advantage of many of the built-in enhancements in more recent releases of OS X, if you run MacVector 14.5 on OS X 10.6, you will find there are certain limitations;
  • (i) The mouse pointer does not change in a context-sensitive way when moving over different interface graphical items.
  • (ii) Tool tips within the editors do not display.
  • (iii) The Feature tab list only display the first qualifier for each feature (but if you double-click to open the editor, you will see that all of the qualifiers are present).
  • (iv) The Primer Database selection popup scrolling menus are not available – you should instead open the actual .nsub file and copy the primer sequence from there.
  • (v) The Sparkle automatic online updater is non-functional.

New in MacVector 14.0.6 (Nov 6, 2015)

  • Bug Fixes:
  • The fix to the “one-out” RE site numbering in MacVector 14.0.5 inadvertently caused a problem where the junction of cloning events was not correct if the sticky ends were generated by different, but compatible, enzymes. This has now been fixed.

New in MacVector 14.0.5 (Oct 30, 2015)

  • Bug fixes:
  • A “one-out” bug in the displayed numbering of Restriction Sites in the Map tab has been fixed.
  • You can now correctly activate licenses running OS X 10.6.8
  • A bug resulting in bootstrap phylogenetic reconstruction trees having branch values of greater than 100% has been fixed.
  • A hang whilst opening sequence files containing certain combinations of features has been resolved.
  • Circular sequences no longer open in linear mode if the last sequence you opened was a linear molecule.
  • Zooming a circular sequence no automatically longer maxes out at 9.8” radius.

New in MacVector 14.0.4 (Aug 31, 2015)

  • Bug Fixes:
  • A crash when selecting from the first residue in a multiple sequence alignment has been fixed.
  • A problem with “ghost highlighting” in the multiple sequence alignment editor has been resolved.
  • Any phrap parameter changes you make are now remembered in the preferences file to simplify repeated analyses of similar datasets.
  • A number of minor changes have been made to the Find dialog, Feature Editor and some Analysis dialogs to smooth out certain common workflows.
  • The green “zoom” button has been removed from the floating Graphics Palette to prevent you accidentally clicking on it and ending up with a giant window that cannot be easily resized.
  • Using File | Export to export contigs from an assembly project in Fasta or Fastq format now only includes the consensus sequence of each contig.

New in MacVector 14.0.3 (Jul 17, 2015)

  • Bug Fixes:
  • A bug where importing fasta files into the multiple sequence alignment editor would leave the last sequence blank has been fixed.
  • You can now Digest a product from the primer results Map tab and the predicted product will be placed on the Cloning Clipboard.
  • The Free-form feature editor input edit box now wraps.
  • /label features are now displayed in the Map tab as per version 13.5.5.
  • You can now use apostrophes in feature qualifier values.

New in MacVector 14.0.2 (Jul 8, 2015)

  • Minor Enhancements:
  • There is a new setting in the Preferences->Colors pane that gives you more control over the coloring of Features in the Editor tab.
  • Bug Fixes:
  • The ORF Analysis text result view now correctly displays the detected ORF translations./label
  • has been restored as a valid GenBank qualifier. Note that this qualifier is no longer endorsed by the NCBI but has been extensively used by MacVector users so we now consider it to be a MacVector extension of the official format.

New in MacVector 14.0.1 (Jun 27, 2015)

  • Bug Fixes:
  • Application “hangs” when invoking Select All in the Contig Editor and when deleting a segment of a Feature have been resolved.
  • A minor glitch in the Restriction Enzyme editor has been fixed – in some cases that could cause a crash when displaying the non-cutters results.
  • You can now paste sequence data into an empty Map tab without MacVector crashing.

New in MacVector 14.0 (Jun 23, 2015)

  • 64-bit Architecture:
  • MacVector is now a fully 64-bit application. The main utility of this is that MacVector can take full advantage of all of the memory installed on your computer, allowing it to handle larger sequences and alignments. This is most noticeable in the Multiple Sequence Alignment, Align To Reference and Assembler functions where longer reference sequences and increased numbers of (e.g.) fastq-formatted Reads can be imported and aligned.
  • The move to 64-bit has also allowed much longer sequences to be viewed in the Align To Reference editor – previously, sequences would not display properly when scrolling
  • horizontally past about 2,000,000 base pairs.
  • MacVector14 is no longer dependent on the deprecated “CarbonLib” compatibility library. This helps ensure that MacVector will continue to work with future releases of OS X where this library is likely to be removed.
  • Primer Database Support:
  • MacVector now directly supports the concept of a “Primer Database”. There is a new Primer Database.nsub file installed in the /MacVector/Subsequences/ folder, populated with a number of common universal primers. This is used as the default database file, but you can easily choose any file of your own, or add your own primers to this file, or to a copy of it. The Analyze menu has been streamlined to remove the old Primers submenu.
  • Primer Database Search – this is a new function in the Analyze menu. Its is similar to the Nucleic Acid Subsequence search function, except that it uses Primer Database.nsub as the default search file and has a few extra settings to simplify handling primers with tails and/or mismatches to the target sequence.
  • Quicktest Primer – this now lets you save primers direct into the current primer database and also lets you retrieve primers from the database via a simple popup scrolling menu.
  • Primer Design (Primer3) – you can now select primers in the spreadsheet result window and add them to the primer database and select primers from the database using the popup scrolling menu.
  • Assembler Bowtie Improvements:
  • Bowtie has been updated to support version 2 which can handle gaps in the aligned reads. This allows the use of much longer input reads (which typically have more indels) and provides far more accurate coverage information because, with the older version, reads with indel mismatches would be discarded even if they were "real" matches.
  • Miscellaneous Enhancements:
  • The Primer Design (Primer3) “Test” mode now has a text output similar to the old Test PCR Primer Pair functionality, allowing you to view details of all of the possible products generated by the pair of primers.
  • There are some cool new "Rounded Rectangle" feature graphics types.
  • You can now directly select residues in the Map view in the default "zoom" mode. This lefts you use the Map tab for all editing operations except for actually typing residues (but you can select then click on the Editor tab to do that).
  • MacVector now supports the new Regulatory GenBank feature type.
  • You can import features into a sequence with files formatted using the Sequin Table
  • format.
  • More options in the way the sequence Editor and Map views are initialized are now saved to preferences so that MacVector “remembers” how you like to view your sequences.
  • The cut sites and recognition sequences of restriction enzymes and now listed in the text outputs.
  • Colored residues or background in the single sequence Editor tab are now only displayed if the underlying feature is located on the sequence line. This provides much finer control over which regions of the sequence you would like to see highlighted in color.

New in MacVector 13.5.5 (Mar 3, 2015)

  • Bug Fixes: A problem where features of type “????” would be created when opening a saved Align To Reference (.axml) file has been resolved.

New in MacVector 13.5.4 (Feb 24, 2015)

  • Bug Fixes: The Quicktest Primer fix from 13.5.3 inadvertently disabled the “mouse-over” restriction enzyme display functionality. This has been restored.

New in MacVector 13.5.3 (Feb 18, 2015)

  • Bug Fixes:
  • The Contig Editor display now refreshes correctly on OS X 10.6 when loading a saved alignment.
  • A crash has been fixed in the Protein Analysis Toolbox.
  • A crash in the Quicktest Primer interface when working with large numbers of restriction enzymes has been fixed.

New in MacVector 13.5.2 (Jan 17, 2015)

  • Bug Fixes:
  • A scrolling issue in the Contig Editor/Align To Reference Editor has been resolved. A rare crash when awaking on a different network has been fixed.

New in MacVector 13.5.1 (Dec 6, 2014)

  • Bug Fixes:
  • On OS X 10.6, imported sequences now retain their original file name.
  • An occasional crash closing modified sequences that were not saved has been fixed.
  • Translations in the annotated text output now correctly honor the preferences flags.
  • Some inconsistencies in the numbering of “untitled” sequences has been resolved.
  • A problem where sequence windows would disappear under OS X 10.6 has beeen resolved,
  • A number of display glitches in the Align To Reference editor have been fixed.
  • A problem where translations were sometimes missing in the Map tab when zoomed to the residue level has been fixed.
  • The ability to import BAM files into an Assembler Project has been restored.
  • Nucleic acid multiple alignment documents now have their own color group and blocking defaults.
  • Primers in the “Test PCR Primer Pair” mode of Primer Design can now be over 35 nt in length.
  • Text views now automatically resize in width to print on a single page.

New in MacVector 13.5 (Nov 4, 2014)

  • Overview:
  • The graphics Symbol Editor and floating Graphics Palette have been rewritten in preparation for MacVector moving to a 64-bit architecture (due with MacVector 14.0). The other main enhancements have been aimed at better handling of Next Generation Sequencing (NGS) files, particularly with the Align To Folder and Assembler Velvet de novo assembly functionality. There has also been significant code optimization to better handle the analysis of large genomic sequences, particularly noticeable with the Pustell Matrix “dot-plot” functionality.
  • Align To Reference Enhancements:
  • The Align To Reference alignment algorithm and the Editor now handle alignments around a circular sequence. Note that this is only the case for the Sequence Confirmation algorithm. The cDNA Alignment algorithm still assumes the target sequence is linear.
  • You can now select one or more sequence “Reads” in the Align To Reference Editor and save those reads to a fasta or fastq formatted file by choosing File | Export… and selecting the required format in the resulting dialog. The primary benefit of this new feature is that you can now run alignments of up to 500,000 NGS reads against a reference sequence and then specifically export all of the aligned (or non-aligned) reads for further analysis.
  • Align To Folder Enhancements:
  • Align To Folder can now perform alignments against fasta and fastq files with many millions of reads. On a relatively new laptop, a search of a 1kb sequence against a ~2.5 MB fastq file containing 10 million 100nt reads takes about 40 minutes.
  • You can now retrieve the “hits” from an Align To Folder run to one of three destinations – the MacVector desktop (i.e. opening each hit in a window on the screen), to a folder (where each hit is written out as a separate file) or to a single file (where the hits are concatenated into a single fasta or fastq file). The key to this functionality is that you can select lines in the Folder Description List window as follows;
  • When any part of a line is highlighted, that “hit” is considered “selected”. You can then choose one of the options from the Database menu;
  • Database | Retrieve To Desktop – this opens windows on the desktop containing the selected sequences. If the matching sequence was a single file (e.g. in MacVector or GenBank format) the original file is opened. If the hit is a Read within a large fasta or fastq file, a new sequence window is created and populated with the Read sequence.
  • Database | Retrieve To Disk – this saves the hits to individual files in the selected destination folder. If the matching sequence was a single file (e.g. in MacVector or GenBank format), the file is simply copied to the destination so that all features and feature appearance information is maintained.
  • Database | Retrieve To File – this saves the sequence information (plus any quality information in the case of fastq data) of all selected hits into a single file in either fasta or fastq format.
  • Taken together, these enhancements let you use Align To Folder to pull out rare matching reads from large NGS datasets for use in further analysis or DNA Assembly. In beta testing, this has been used to “clone” genes from MiSeq RNA-Seq runs using Protein source sequences aligned to fastq NGS data.
  • Pustell Matrix (“Dot Plot”) Enhancements:
  • The performance of large (i.e. genome-sized) Pustell Matrix dot plot alignments has been dramatically improved. You can now scan and display pairs of bacterial genomes in just a few seconds to easily identify inversions, duplications and rearrangements in their gene organization. You can zoom in and out of the dot plot display in real time to explore the relationships right down to the residue level. If you are using large sequences, consider increasing the Hash Value, Window Size and Min % Score values to speed up the calculations. For example, the plot below comparing two E. coli genomes was generated in just a few seconds using Hash Value=12, Window Size=100 and Min % Score=85.
  • Nucleic Acid Subsequence Enhancements:
  • A small but significant change has been made to the graphical output of this. If you select a pair of hits in the Map results tab, then choose Edit | Copy, the sequences of the actual subsequences are substituted into the copied sequence. This allows you to maintain primers in a nucleic acid subsequence file and use the Nucleic Acid Subsequence analysis option to quickly identify and “clone” predicted PCR fragments even if the primers have mismatches or tails added to them.
  • Assembler Enhancements:
  • Reference alignments (from Bowtie) now have a separate coverage report tab that lists the read coverage for every gene and CDS feature in the reference sequence. You can use this to (e.g.) accurately measure relative expression levels of mRNA in RNA-Seq experiments or plasmid copy number in whole cell DNA sequencing experiments.
  • Velvet now does a much better job at trimming poor quality residues from input sequences.
  • Velvet now handles paired sequences that have identical names.
  • You can now export unassembled reads from Bowtie and Velvet alignments as fasta or fastq files. This lets you filter out reads that match specific sequences so you can focus subsequent alignments using a subset of reads.
  • Miscellaneous Enhancements:
  • You can now reset the circular origin of circular sequences to any arbitrary position. Simply click between the residues where you want the new origin to be, then right-click (or -click) and choose Set Circular Origin from the popup menu.
  • Informative tooltips have been restored in all views. There is a setting to turn this on/off in MacVector | Preferences | General.
  • The cDNA Align To Reference algorithm now does a much better job of displaying segmented reads in the Map view.
  • A number of issues with saving trace files have been resolved. In particular, you can now use the bsml format to save annotations with chromatogram information.

New in MacVector 13.0.7 (Sep 5, 2014)

  • Bug Fixes:
  • FINALLY tracked down the bug that some of our European customers have been
  • seeing with the multiple alignment color groups! Thanks for your patience on that one, it
  • was related to using French/German/Spanish localization.
  • The residues that appear on the Y axis of a “dot plot” matrix when zoomed in to the
  • residue level are now displayed correctly on all versions of Mac OS X.

New in MacVector 13.0.6 (Sep 3, 2014)

  • Bug Fixes:
  • Velvet now correctly honors the Long Read Threshold setting to distinguish between short and long reads..
  • The codon usage table information is now reset between runs.
  • A bug that caused the DNA color group values to get cleared has been fixed. There may still be another intermittent bug that some users have reported that we have not been able to reproduce.
  • An intermittent crash when repeating certain analysis functions has been fixed.

New in MacVector 13.0.5 (Aug 19, 2014)

  • Bug Fixes:
  • The Multiple Sequence Alignment (MSA) Editor no longer has missing regions in the display when in linear mode with blocking switched on.
  • Printing from the MSA Editor and MSA Picture tabs has been improved for multiple- page printing.

New in MacVector 13.0.4 (Jul 16, 2014)

  • Bug Fixes:
  • The Multiple Sequence Alignment Editor “name” pane can now be resized much narrower to reduce white space when printing.
  • A crash when deleting the entire contents of the Annotations “Comments” section has been resolved.
  • The Align To Reference and Contig Editor Map tabs now calculate and display the selected range (bp) in the Range toolbar item.
  • Clicking to deselect in the Map tab when in “sequence select” mode no longer scrolls back to the top.
  • The Test Sequencing Primer function no longer crashes if multiple alternate binding sites are present in the target sequence.

New in MacVector 13.0.3 (Jun 17, 2014)

  • Bug Fixes:
  • BLAST now works on OS X 10.6
  • A crash when opening multiple sequence alignment files containing terminator characters
  • (*) has been fixed.
  • A problem where features with no description could crash MacVector has been fixed.

New in MacVector 13.0.2 (May 31, 2014)

  • Bug Fixes:
  • A critical crash bug encountered during delete/paste/reverse+complement operations in feature - rich sequences has been fixed.
  • Repeat invocations of the Analyze | Translate function now work as expected.
  • Zooming in the Map tab of sequences when the line length is set to “unlimited” now works correctly.
  • Base Composition plots have been re-enabled.

New in MacVector 13.0.1 (May 9, 2014)

  • Bug Fixes:
  • The various “Fit To Printer Page” actions in MacVector (Preview in the single sequence
  • Map tab, the Fit To Print options in the Chromatogram editor and the Fit To options in
  • the Phylogenetic Tree Window) now all respond correctly after Page Setup has been
  • used to change paper or print orientation.
  • The correct primer is now copied after sorting then copying primers in the Primer
  • Design Spreadsheet window.
  • The feature numbering in the Features tab now correctly responds to changes in the
  • numbering origin of linear sequences. This also fixed a bug where features that became out of range disappeared after insertions and deletions and other numbering became corrupted.
  • Changing the topology now correctly changes theMap from linear to circular (or vice-
  • versa) on all versions of the OS.
  • The cloning clipboard Digest function now works on OS X 10.6.
  • Changing preferences in the multiple sequence alignment window now correctly flags the underlying document as dirty.
  • The Phylogenetic window Export Tab Contents As menu item is now enabled and lets
  • you export the tree in a number of different graphical formats.
  • The Align To Reference Editor tab now displays the numbering for traces aligned to the
  • minus strand.
  • The Reverse Translation function now lets you create probes longer than 15 nt.

New in MacVector 13.0.0 (Apr 9, 2014)

  • Interface Enhancements:
  • All of the toolbar icons have been reworked to have a more consistent look and feel and to display at high resolution on Retina screens.
  • The tab bars have been redesigned on all of the primary windows.
  • All result windows now get collated into a single result window per sequence, with tabs for each result. If you want to view more than one result at a time, you can “tear off” any tab into its own window.
  • There is a new File | Export Tab Contents menu item that can be used to save tab- specific data (e.g. graphics or text).
  • Primer Design Enhancements:
  • The Quicktest Primer interface now shows restrictions enzyme cut sites in the parental sequence around the primer binding site.
  • The Quicktest Primer interface also shows “one out” restriction enzyme sites. These are colored according to the effect that changing the mismatched base would have on any overlapping annotated ORFs . Potential silent mutations, which would not change the amino acid sequence of any coding sequences, are shown in red, those that would change the code are shown in green.
  • Hovering over a restriction site with the mouse displays the actual recognition sequence of the site.
  • Clicking and holding on a site, temporarily changes the sequence of the primer to match the mutated site and changes to the amino acid sequence of any ORFs are displayed above the sequence.
  • Double-clicking on a one-out site changes the primer sequence to match the selected site.
  • The Primer3 interface has been enhanced for testing pairs of primers. There is now a fourth “testing” mode that is automatically invoked when a pair of primers are entered. This mode removes most of the constraints to ensure pairs of binding primers are correctly identified.
  • The optimal annealing temperature for pairs of primers is now displayed in the spreadsheet result.
  • Primer3 will now include primers that overlap the ends of the region to be amplified. Previously, primers had to be entirely outside of the region.
  • Assembling de novo NGS Sequences With Velvet:
  • The popular Velvet algorithm has been added to the Assembly module. You can use this to assemble large numbers of NGS sequences supplied in fastq files. In our hands, around 20 million 90nt Illumina reads can be assembled into a 6 Mb bacterial genome in around an hour on a retina MacBook Pro with 16 GB RAM.
  • Apple Scripting:
  • Some basic Applescripting capabilities have been added to MacVector 13. In particular, there are now commands to open and save files in specified formats, so you can create Applescripts that can iterate through a folder of sequences and save each of them into a different folder in any format supported by MacVector. There is a new Applescripts folder with some example scripts to get you started.
  • Chromatogram Files:
  • There is a new Raw Data tab that lists the peak positions, basecalls, quality values and areas under the curve for the chromatogram trace data. There are also columns that indicate the potential presence of “mixed” residues at a variety of confidence levels. It is in a tab-delimited format that can be copied and pasted directly into Excel for additional analysis.
  • Miscellaneous Changes:
  • The Starting Point dialog now has links to the Entrez browser and to help pages to help new users understand the many different ways you can get sequences into MacVector.
  • The Align To Folder function now reads fastq formatted files in the target folder. The Description result window now displays the full name of each sequence, even with the typically long names from NGS experiments.
  • The phrap default parameters have been tweaked to generate better assemblies of both NGS and chromatogram data.
  • All of the “plain text” views now automatically adjust their formatting when printed to ensure that they are no more than a single page in width.
  • The Page Preview and Magnify controls have been moved from the bottom left corner of map windows onto the toolbar.

New in MacVector 12.7.5 (May 25, 2013)

  • Bug Fixes:
  • Edit | Cut now places the cut fragment on the global pasteboard
  • Some long term issues pasting copied fragments containing truncated features that cross
  • the origin of circular molecules have been resolved.
  • Double-headed arrow features are now displayed correctly at the residue level.
  • Features created from a selection where one end is formed from a restriction site that crosses the circular origin are now correctly created and saved.
  • A few issues creating and reading .sqn and .tbl files for use with Sequin have been fixed.

New in MacVector 12.7.4 (May 7, 2013)

  • Deprecated Functions:
  • This is the last release of MacVector that will retain the now obsolete Find PCR Primer Pairs and Test PCR Primer Pairs functions. All of the functionality in these interfaces have been replaced by, and improved upon, by the Primer Design (Primer3) and Quicktest Primer functions. For more information on using these new functions, take a look at the Primer Design Tutorial.pdf tutorial that you can find in the /Applications/MacVector 12.7/Documentation/ folder.
  • Bug Fixes:
  • Contigs generated by phrap assembly now have quality values.
  • You can now use the Find function to search for gaps (make sure you have the “Literal” checkbox selected.
  • A one-out bug displaying the [size] metatag label in Map views has been fixed. Protein sequences no longer display spurious text in the feature labels.
  • Restriction enzyme sites are now correctly regenerated on the cloning clipboard when creating constructs in the flipped orientation.
  • Some display glitches drawing restriction enzyme sites when zoomed in to the origin of a circular plasmid have been fixed.
  • Restriction sites where the cut location is just before the first residue of the sequence are

New in MacVector 12.7.1 (Jan 10, 2013)

  • Bug Fixes:
  • A bug where the numbering of the alternative binding sites in the Quicktest Primer dialog was incorrect for sequences with a non-zero origin has been fixed.
  • A crash problem deleting reads extending beyond the end of the reference sequence in an Align To Reference alignment has been fixed.
  • Creating a misc_feaure from a subsequence analysis result window no longer adds an additional residue to the end of the feature.
  • The reaction conditions parameters are now correctly shared with all algorithms that need to calculate melting temperatures.
  • You can now run Primer3 on sequences with a negative origin.

New in MacVector 12.7 (Nov 19, 2012)

  • Has a new Cloning Clipboard that dramatically simplifies the creation of new DNA constructs. The new functionality not only lets you join molecules together using an intuitive drag and drop interface, but also lets you easily accomplish cloning constructs that were difficult with earlier versions of MacVector.
  • There have been some significant performance enhancements to the Dot Plot (DNA Matrix) analyses and to the Align To Reference analyses, allowing you to now run pairwise alignments of whole genomes in just a few minutes or to align hundreds of thousands of NGS Reads against a reference genome in an hour or so. A full list of the changes can be found in the Release Notes.
  • Cloning Clipboard:
  • There is a new window available called the Cloning Clipboard that maintains a history of the DNA fragments created each time you use the Digest function. For example, if you select two restriction enzymes in a Map tab, then click on the Digest button, the fragment between the sites gets placed on the Cloning Clipboard. You can then join fragments together directly on the Cloning Clipboard by clicking on one end of a fragment and dragging to a different end, as shown in the animation below;
  • You can also join incompatible ends by filling in or cutting back the overhangs and you can create a new sequence window in MacVector by selecting a fragment and clicking Circularize, or by simply double-clicking on a fragment. A selected fragment can also be directly pasted into an existing target vector by highlighting appropriate destination restriction enzyme site(s) and clicking Ligate.
  • Align To Reference Performance Enhancements:
  • A number of operations in the Align To Reference functionality have been optimized to be of more use for aligning large numbers of Next Generation Sequencing reads against large genomes. Importing reads is now very much faster (in many cases 100x faster) and aligning reads is from 5x to 50x faster. With the appropriate parameters, you can now align several hundred thousand reads against a typical bacterial chromosome in just a few hours. Individual edits in the Editor tab with several hundred thousand reads are now effectively instantaneous (previously they could take many minutes while the consensus was recalculated). In addition the text in the SNP tab is generated anywhere from 10x to 1,000x faster than previously. Finally, although generation of the text in the Text tab has also been significantly speeded up (again up to 1,000x) it also now runs as a separate thread so you can cancel the operation if it takes too long. To align short reads against a genome, import the reads from a FastQ file using the Add Seqs button (at this stage, we recommend you keep the number of reads below 250,00), then try the following alignment parameters;
  • Optimized Reverse Translations:
  • There are new options in the Analyze | Reverse Translation dialog, allowing you to optimize codon usage when reverse translating a protein. You can now request that the generated DNA sequence uses only the most popular codons from a given codon bias file, or that the generated sequence should have an overall codon usage that most closely matches the codon bias file.

New in MacVector 12.6 (Jul 3, 2012)

  • Quicktest Primer Interface:
  • There is a brand new interactive primer design interface that lets you quickly view the properties of any primer, see instantly where it binds on any open sequence window and even nudge the primer on a sequence to find the optimal primer characterstics. You can edit the primer to introduce mismatches and see the impact of the mismatches on translations crossing the binding site and even add tails containing restriction site. Finally, you can run Primer3 from the Quicktest dialog to find a matching primer suitable for PCR and copy a DNA sequence containing the predicted PCR product, complete with any mismatches or tails introduced by the primers. The new functionality is invoked from the Analyze |Primers | Quicktest Primer menu item.
  • Feature Import:
  • You can now import features from GFF, GFF3, GTF and BED files. To use this, open the parental sequence and choose File | Import Features. Perfectly duplicated features will be discarded, so you can use this to repeatedly import features from an external source where the features in the source file may be updated from time to time without having to start over from scratch. This feature allows you to import annotation directly from many
  • Genome Browsers such as the UCSC Genome Browser.
  • Phrap de novo Assembly of NGS data
  • The add-on Assembler module has been enhanced to allow phrap assemblies of file-based (i.e. FastQ) formatted sequences. Please see the Assembler Release Notes for more details.
  • Miscellaneous Enhancements
  • The Map graphics layout and drawing performance have been speeded up. In particular, MacVector can now display all of the features from a typical bacterial chromosome almost instantaneously and lets you zoom in and out from interesting regions extremely quickly.
  • You can now edit the LOCUS name in DNA sequences.
  • If you option-click on a Read sequence in the Align to Reference Editor, the corresponding trace chromatogram will slide into view in the lower multiple-trace pane. This is particularly useful if you have hundreds of aligned clonal variants and want to quickly inspect the chromatogram to validate mutations.
  • Sorting an Align to Reference assembly now ensures assembled Reads always float to the top.
  • All Tm calculations now use the updated thermodynamic nearest neighbor parameters of Santa Lucia (1998) and also take into account divalent cation concentration and dNTP concentrations as described by von Ahsen et al (2001).
  • You can now save all open sequences into a single GenBank file – simply open all the sequences of interest, choose File | Save As, then choose GenBank from the format menu and set the Window parameter to “All open sequences”.
  • The Analyze | Translation output now has an additional option to provide more flexibility in the annotated sequence display so that you can force the display of a defined region within the context of the entire sequence.
  • The label that is displayed for each feature on sequence Maps is now much smarter to help cut down on the amount of text that is displayed by picking out and displaying selected qualifiers for certain common feature types.
  • The contents of the multiple sequence alignment Editor tab are now copied to the clipboard as a graphical image when nothing is selected and you choose Edit | Copy.
  • The Map results of Analyze | Subsequence searches now automatically show hits on the plus strand above the sequence and hits on the minus strand below the sequence.
  • Import of plain DNA sequences (ASCII or FastA) with lots of N’s is now handled better so users are not prompted to select the type of sequence.
  • The maximum size of a primer that can be searched for or tested in all of the primer design functions has been increased to 80, except for Primer3 which has an internal limit of 35.
  • The Auto-Annotation function can now handle finding features that are less than 20nt in length.
  • The Pustell Matrix analysis functions have now been moved under an Analyze | Create Dot Plot sub menu. The DNA:DNA matrix now has a maximum ktup value of 12 – use this to rapidly generate dot plots comparing whole bacterial genomes (analysis time is cut to seconds rather than hours).
  • Non-sequence characters are now stripped out of text pasted into the Find and Test PCR and Sequencing primer dialog boxes.
  • You can now run T-Coffee on long alignments (e.g. 10,000 residues or more) without it running out of memory.
  • New sequences can be imported with full annotation by the copy and paste of GenBank, EMBL and FastA documents.

New in MacVector 12.5.1 (Jan 20, 2012)

  • Several occasional crashes have been fixed.
  • Printing from the multiple sequence alignment editor now no longer prints additional blank pages.
  • A bug leading to corrupted data when copying and pasting items between Restriction Enzyme documents has been fixed.
  • The CDS translations display in the single sequence editor now updates correctly when residues are inserted before CDS features in the editor.

New in MacVector 12.5 (Dec 13, 2011)

  • Reference Alignments of Next Generation Sequencing Data:
  • The add-on Assembler product is now able to align millions of reads from next generation sequencing projects against one or more genomic reference sequences. Please see the Assembler 12.5 Release Notes for more details
  • New Multiple Sequence Alignment Algorithms:
  • DNA and Protein sequence alignments can now be automatically aligned with the popular T-Coffee and Muscle alignment algorithms as well as the existing ClustalW algorithm.
  • Alignments are now scored using the matrix selected in the ClustalW parameters dialog. Scoring is calculated by adding the scores of each pairwise alignment in the multiple alignment.
  • Rewritten Windows:
  • The restriction enzyme, proteolytic enzyme, DNA and protein subsequence editors and the Matrix editor have all been rewritten using Cocoa table views. Apart from an improved appearance, this change makes it easier to navigate and select entries in the editors, simplifying the creation of subsets (you can copy and paste between windows). In addition, you can sort the columns by clicking on the titles.
  • The Entrez browser has been rewritten and now permits an unlimited number of search terms to be combined for a search.
  • Sequence Window Enhancements:
  • There are new “Segmented Hollow Arrow”, “Segmented Hollow Box” and “Segmented Full Height Hollow Box” symbol. You can use these for segmented features (e.g. CDS features containing introns) in the Map tab and the exon segments will be shown joined by a line e.g.
  • The Editor tab can now display the translations of CDS features above or below the sequence – turn this on using the Strands button.
  • Miscellaneous Enhancements:
  • Segmented subsequence matches now have all segments displayed in the text and graphical outputs. This lets you e.g. search for canonical E. coli promoter sequences and see both the -35 and -10 regions displayed in the Map.
  • The Align to Reference algorithm now runs as a standard job so that you can switch to other windows and carry on using MacVector while waiting for lengthy alignments to complete.
  • When using a Roaming license off the network, there is no longer a temporary hang when MacVector attempts to reconnect to the license server.
  • Many dialogs have had error handling code added so that red information text will be displayed explaining why the OK button is not enabled if invalid parameters have been entered.
  • The maximum number of results that can be returned by the Align to Folder function has been increased to 32,767.
  • The SNP tab of the Align to Reference Window now lists all of the changes between the consensus and the reference sequence and includes the codon change and amino acid change of any CDS feature crossing each SNP.

New in MacVector 12.0.6 (Oct 12, 2011)

  • Cumulative patch release that fixes a number of important bugs in earlier releases of MacVector 12.0.

New in MacVector 12.0.5 (Aug 17, 2011)

  • The installer now installs writable codon bias table files and the code has been changed to ensure the Nucleic Acid Toolbox functionality works even if those files are read only.
  • The floating graphics palette window now stays hidden when set that way.
  • Asymmetric restriction enzymes sites now copy correctly from one enzyme list window to another.

New in MacVector 12.0.4 (Jul 23, 2011)

  • Bug Fixes:
  • Find searches using the “literal” flag now correctly finds matches on the reverse strand.
  • Sequences containing more than 32766 features can now be downloaded and saved from the Entrez database browser.
  • Incorrect error messages displayed by Primer3 when it actually ran successfully have been removed.
  • A problem with the LOCUS line when saving new sequences in GenBank format has been fixed.
  • Staggered restriction sites in the map view now display correctly when on the complementary strand.
  • The Feature list no longer resets to the top after editing a feature. The “Forward-delete” button now works as expected in the Trace editor.
  • The performance of the multiple sequence alignment editor has been improved so that you can now easily edit alignments containing thousands of sequences with no lag.
  • The Generate Transcript function now correctly handles sequences with non-zero origins. MacVector is now more tolerant importing GenBank files with malformed LOCUS lines.

New in MacVector 12.0.3 (Apr 29, 2011)

  • Some problems with the Align to Folder alignment output incorrectly displaying reverse- complemented matches have been resolved. A problem where the Primer3 algorithm would fail with the error "Illegal value for INCLUDED_REGION" has been fixed. The Contig Editor now always provides a vertical scrollbar to prevent the occasional problem where Reads would be scrolled off-screen with no easy way to view them. The restriction enzyme output window has been reworked to ensure asymmetrical cleavage enzymes are always reported consistently. A bug where the cDNA Align to Reference algorithm would occasionally freeze with certain base combinations has been fixed. The Assembly Editor now highlights the editable sequence when you select objects (open reading frames, primers etc) in result windows, allowing you to then

New in MacVector 12.0.2 (Mar 3, 2011)

  • Find now correctly finds matches at the very end of a sequence. Find now finds matches that cross the circular origin.
  • The Align to Reference “Remove Seqs” toolbar icon now becomes enabled when one or more sequences are selected.
  • Find matches in the Align to Reference editor now stay highlighted. The Align to Reference editor no longer deselects after a copy operation.
  • An occasional problem where restriction sites would be duplicated near the origin of circular sequences has been resolved.
  • Feature data is no longer left on the clipboard when you copy a text sequence from outside of MacVector.
  • The graphics palette now allows entering of radius values in cms and points.
  • Sequences with a mixture of upper and lower case residues can now be saved in GenBank, FastA, GCG and EMBL formats without losing the lower case residues.

New in MacVector 12.0.1 (Feb 12, 2011)

  • Selecting items in the Symbol Editor treee view now selects them in the Map view.
  • The subsequence editor now correctly saves newly created subsequences so that they are included in subsequence searches.
  • Chromatogram files are now saved correctly as SCF files by default.
  • Align To Reference assemblies are now saved in the correct default format after being edited.
  • A number of crashes when using Align To Folder to search in folders containing non- sequence files have been fixed.
  • Restriction Enzymes and Subsequences are now displayed alphabetically in their respective editor windows.

New in MacVector 12.0 (Feb 8, 2011)

  • Enhanced Circular Sequence Support:
  • While MacVector has always been able to display and analyze circular sequences, MacVector 12 has added a number of significant enhancements. You can now select across the 12 o’clock origin of circular sequences and features can seamlessly span the origin. The order that you select features or Restriction Enzyme sites is now important – the selection is propagated in the clockwise direction. Most algorithms are now completely circular sequence aware, allowing you to e.g. find open reading frames that cross the origin, or select a region that crosses the origin for analysis.
  • Enhanced Graphics:
  • The Map graphics has had a huge amount of work;
  • There is a new collapsible overview pane that displays a full-length miniature version of the sequence so that you can orient yourself when zoomed into a long sequence.
  • Graphics Palette
  • The graphics palette has been rewritten with a lot of new functionality;
  • Selection Modes – a row of buttons lets you choose between the following selection modes;
  • (a) Zoom – this is the default and the mode used by older versions of MacVector – you can click on features or sites to select them and if you click, hold and drag, the display resets to “zoom in” to the segment you selected.
  • (b) Feature Selection – clicking and dragging selects all the features or sites that are touched by the selection rectangle.
  • (c) Sequence Selection – clicking and dragging selects just the sequence touched by the selection rectangle.(d) Magnify – clicking magnifies the display 2-fold. -clicking reduces the magnification 2-fold.
  • (e) Slide – this mode lets you drag the current zoomed region to the left or right. You can also use this to rotate circular sequences so that any arbitrary location is set to the 12 o’clock position.
  • (f) Copy Feature Appearance – this mode is only available if you have one or more features selected. Once selected, if you then click on a different feature, all the selected features will change appearance to match that feature.
  • Quick Fit Buttons – four buttons let you quickly adjust the display to useful range and scaling;
  • (a) Zoom to Sequence – adjusts the residues per inch so that the residues are just visible. Does not change the current displayed sequence range.
  • (b) Fit To Window – adjusts the residues per inch so the entire sequence range can be displayed in the window.
  • (c) Fit To Page – adjusts the residues per inch so the entire sequence range can fit on the currently selected printable page.
  • (d) Fit Residues – this resets the displayed range to the entire sequence and adjusts the residues per inch so that residues are just visible.
  • Navigation Buttons – these let you scroll around in the Map graphic;
  • (a) Slide Left – if you have a range selected, this nudges the range to the left. Full circular molecules are rotated slightly to the left. The left arrow key also performs this function.
  • (b) Slide Right - if you have a range selected, this nudges the range to the right. Full circular molecules are rotated slightly to the right. The right arrow key also performs this function.
  • (c) Home – this centers the current range in the top center of the window and resets rotation of circular molecules.
  • (d) Zoom In – this zooms in so the displayed range is reduced 2-fold.
  • (e) Zoom Out - this zooms out so the displayed range is increased 2-fold.
  • (f) Reset Zoom – this resets the zoom so the entire sequence is displayed and fits it to the window.
  • To make room for all the new buttons, a number of infrequently used buttons (e.g. shadowing and anti-aliasing control) have been moved to Map View Preferences pane.
  • Symbol Editor
  • The symbol editor has been completely rewritten for MacVector 12. There are new symbol types (“Delimited Line”, “Full Height Hollow Box”, “Simple Line” and “Single Arrow No Drop”) and new “meta tags” that can be accessed by clicking on a drop down arrow to the right of the Label edit box.
  • Sequence Display
  • You can now display sequences at the residue level in double-stranded form.
  • When at the residue level, restriction enzyme sites are displayed with the actual cut sites ends displayed on the sequence. If you select a restriction fragment, the highlights clearly show the structure of any staggered ends.
  • There is now the option to display the actual sequence of certain types of features – in particular, you can show the amino acid sequence of CDS features aligned above or
  • below the DNA sequence. Other features that can be displayed as residues are RNA features and the primer_bind feature type.
  • Sequence Editor Enhancements:
  • There is now the option to color the sequence in the main Editor tab. This is controlled through the Preferences->Colors pane. Any features that are visible in the Map tab are displayed in color in the Editor when this is enabled.
  • You can also select a range in the editor, then choose Edit->Transformations->Color: to set that range to a color of your choosing.
  • The Editor now supports the use of lower case characters. You can mix and match upper and lower case characters to indicate regions of interest and the appropriate case will be used in all printed output. You can change the case of any selected region using the items in the Edit->Transformations menu. Note that the case of the sequence does not have any effect on any of the analysis functions.
  • The search function has been reworked to simplify searching both strands for a sequence. The search will now correctly find e.g. primer sequences on the minus strand using the default settings.
  • Restriction Enzyme Enhancements:
  • There is now the option to search for “one out” restriction enzyme sites by selecting a checkbox in the restriction enzyme analysis dialog. These are displayed in a more pastel color shade than normal sites and have an asterisk appended to distinguish them in text lists.
  • Unique Restriction Enzyme sites in a molecule are now shown in Red.
  • If you double-click on a Restriction Site, all of the sites of that type (e.g. EcoRI, BamHI etc) will be selected so you can quickly see where all the sites of a particular type lie on the sequence.
  • If a DNA fragment with “sticky ends” has been copied to the pasteboard using Edit- >Digest, then sites in the Map view are highlighted with pastel red and/or green to indicate which end of the fragment they are compatible with.
  • Miscellaneous Enhancements:
  • The Contig, Align to Reference, Trace and Multiple Sequence Alignment Editors have all been rewritten to use Quartz graphics resulting in higher quality displays and printouts and images that are copied to the pasteboard using the OS X standard PDF format.
  • You can now sort sequences in the Align to Reference editor.
  • There is a new SNP report tab in the Align to Reference window. This lists all of the potential SNPs that are present in the aligned reads. For chromatogram files, the algorithm considers the area under the curves to determine which SNPs appear “probable” and which SNPs are “possible”.
  • Many analysis results (e.g. Restriction Enzyme, Subsequence, ORF and Primer3) can now be easily converted to permanent features by right-clicking (or -clicking) on the result object and choosing “Create xxx Feature” from the context-sensitive menu (xxx will be substituted by the appropriate feature type).
  • You can also drag result objects and drop them on the parent window to automatically create a corresponding permanent feature.
  • Assembly projects can now have their contents (contigs and unassembled reads) exported in FastA format (choose File->Export As...).

New in MacVector 12.0 Beta 8 (Jan 12, 2011)

  • Virtual Cloning is much easier with auto detection of compatible sites. The whole interface has been reworked with a graphical overview of your entire sequence making it far easier to visualize and navigate around your sequence.

New in MacVector 11.1.2 (Jul 28, 2010)

  • Translations now correctly honor the genetic code shown in that dialog rather than the global genetic code.
  • You can now suppress the automatic re-ordering of reads in the Align to Reference window by holding down the key when clicking on the OK button in the align dialog.
  • Trace files now print correctly.
  • BLAST matches to the complementary strand are now correctly numbered in the alignment text output window.
  • Restored the ability to read GeneWorks files.
  • Fixed an occasional crashing bus in the graphics display when editing a feature when the corresponding automatic Restriction Enzyme file was also open.
  • A bug where switching between Advanced tabs in the Primer3 dialog and editing one of the numeric fields would cause a crash has been fixed.
  • The annotated sequence text output now strips “/note=” from the front of any feature description text. This means that only the actual text you type into the Feature Editor Free-Form tab will now be displayed as the label for the feature.
  • MacVector can now open files saved from previous versions that had truncated LOCUS lines.
  • The ability to use non-ASCII Mac-Roman characters (e.g. ∆, ® and ©) in Feature descriptions has been restored.
  • Printing annotated sequences from the Editor tab now displays the correct translations.
  • Cross_match now takes quality values into account when evaluating the most likely insert segment in a Read.

New in MacVector 11.1.0 (Feb 11, 2010)

  • General
  • Many of the analysis functions now use drop down window-modal sheets rather than application modal dialogs, allowing you to continue to work with other windows to prepare, view or copy data required for the analysis. Many of the sheets have a convenient new history combo box that keeps track of the various data files or target folders used in the dialog to allow rapid switching between commonly used files.
  • Multiple levels of Undo have been added to the Trace, Multiple Sequence Alignment and Contig/Align to Reference editors. All three have also had extensive work to streamline workflows, add keyboard navigation and fix various display glitches and crash bugs.
  • Dialogs to locate auxiliary data files (Restriction Enzymes, Matrices, Codon Bias tables etc) now all default to the appropriate location in the MacVector distribution folder.
  • Align to Folder, Restriction Enzyme, Proteolytic Enzyme, Nucleic Acid Subsequence, Protein Subsequence, Translation and Reverse Translation are now all window modal dialog sheets.
  • You can now drag a selection from one sequence window and drop it into another single sequence window or into an external application (e.g. TextEdit or Microsoft Word) that can accept drag and drop text.You can also drag selected text out of a result window and drop it into other acceptor windows e.g. Microsoft Word or Text Edit (OS X 10.5 and above only).
  • Subcloning
  • You can now select any graphical object (e.g. a feature) and Edit | Copy will copy a blunt ended copy of the underlying sequence to the clipboard.
  • The Ligation dialog now treats sequences copied from external sources or the sequence editor as blunt-ended fragments.
  • Restriction/Proteolytic Enzyme – you can now specify the minimum number of cuts as well as the maximum number of cuts when filtering (or setting up) the results. The selected enzyme data file is now displayed in a history control so you can quickly swap between commonly used files. (see screen shot above)
  • Sequence Analysis
  • Protein Analysis Toolbox – the AA Composition, pI and MW protocol now also displays the predicted extinction coefficients and aliphatic index. In addition, the pI and molecular weight calculations have been revised for increased accuracy.
  • NA/AA Subsequence – the graphical Map result window is now linked back to the parent sequence so that selections in the result window are propagated to the parent editor.
  • The Subsequence editor has been reworked as a dropdown dialog sheet and you can now copy/paste into the Sequence edit box. These changes let you easily paste primers from external applications or from other MacVector windows into a subsequence file to maintain a database of useful primers.
  • There is a new “Show Dots” button that can optionally be added to the MSA editor toolbar (right-click on the toolbar and choose Customize Toolbar… to add the button). This represents matching residues in an alignment with dots rather than the residue itself.
  • Align to Folder – now scans hierarchical sub-folders as well as the selected folder.
  • There is a new Genetic Code reference window accessed from the Window | Genetic Code Key menu item that displays the codons of the currently selected genetic code for quick reference.
  • Features
  • The Feature tab has a new context sensitive (right-click) menu item that lets you join two or more selected features of the same type.
  • The Feature tab context menu now lists all /db_xref and /protein_id qualifiers – selecting one will open the appropriate database source in the default web browser.
  • The labels “Create” and “Remove” are now used consistently throughout MacVector for all buttons that add/create or delete/remove features. This avoids conflicts with labels for buttons that add and remove sequences from an alignment.
  • Miscellaneous
  • Vector NTI .ma4 and .pa4 files can now be imported into MacVector.
  • If you have Growl installed on your machine, the Job Manager will use Growl notifications when a job has completed rather than bounce the icon in the dock.
  • There are now keyboard shortcuts to switch between tabs – hold down the apple command key and type “1” to switch to the first tab, “2” for the second tab etc.
  • “Dirty” windows now display a dot in the red window close button.
  • Text windows and tabs now support standard keyboard and mouse selections.

New in MacVector 11.1 FC4 (Feb 1, 2010)

  • Rather than add just a few major new features for MacVector 11.1, we have instead added a large number of minor enhancements throughout the entire application, all designed to either fix longstanding bugs, improve the Mac OS X look and feel of the application or simplify and improve existing workflows.
  • Many of the analysis functions now use drop down window-modal sheets rather than application modal dialogs, allowing you to continue to work with other windows to prepare, view or copy data required for the analysis. Many of the sheets have a convenient new history combo box that keeps track of the various data files or target folders used in the dialog to allow rapid switching between commonly used files. Multiple levels of Undo have been added to the Trace, Multiple Sequence Alignment and Contig/Align to Reference editors. All three have also had extensive work to streamline workflows, add keyboard navigation and fix various display glitches and crash bugs.
  • The specific enhancements and bug fixes in MacVector 11.1 are listed at http://www.macvector.com/AAATTT/Resources/MV11.1ReleaseNotes.pdf , broken out by functional area. It’s a long list, but if you read it through you should get a lot of hints on how to make the most of this release of MacVector.

New in MacVector 11.0.4 (Oct 28, 2009)

  • You can now print from the Protein Analysis Toolbox graphical result window.
  • The feature range popup-menu control that accidentally got broken in 11.0.3 now
  • works correctly.

New in MacVector 11.0.2 (Sep 22, 2009)

  • The Analysis Toolbar now gets positioned correctly on screens 1024 x 768 and smaller.
  • Any existing unselected contigs in an Assembly Project no longer get dissolved when you run phrap with different sequences selected.
  • When you select individual segments in a cDNA Align To Reference alignment, the selection is now correctly reflected in copies, analysis functions and feature creation dialogs.
  • A crash when deleting the last residue of a Read in the Contig Editor has been resolved.

New in MacVector 11.0.1 (Sep 22, 2009)

  • The Auto Annotation algorithm no longer hangs if it encounters non-sequence files in the source directory.
  • Align to Folder no longer crashes when the target folder contains protein sequences.
  • Printing of chromatogram traces has been restored.
  • You can now paste text-based sequences containing gaps.
  • The translation algorithm is now correctly enabled when the source sequence has a non-zero origin.
  • You no longer get prompted to save unchanged abi trace files when you close the window.
  • Sequence windows now open with double-stranded display turned off by default.
  • When you turn the Analysis ribbon toolbar off, it now stays off the next time you start MacVector.

New in MacVector 11.0 (Aug 21, 2009)

  • Auto Annotation - How often have you received or downloaded a vector or other DNA sequence that has no annotations? The new auto annotation function in MacVector 11 can scan a folder full of existing annotated sequences and automatically add matching features to the bare sequence. Not only does the algorithm add the features, but it also copies the appearance information of the matching features so you can be assured that e.g. an ampicillin resistance gene is always a blue arrow, an M13 origin is always a striped red box etc.
  • Click Cloning Enhancements - In MacVector 11 you can manipulate the ends of restriction fragments before joining them together. A new interface lets you cut back or fill in each end of the source or target molecule before ligation.
  • Floating Analysis Toolbar - For those users who prefer to click on toolbar buttons to initiate analyses, MacVector 11 introduces a new floating toolbar window containing buttons for all common MacVector analysis functions. You can customize the toolbar to show just the functions you use most often or show them all for rapid access to every available algorithm. You can also add analysis buttons to the toolbars of normal sequence windows for ready access to commonly used functions.
  • Sequence Editor Changes - The primary sequence editor has been rewritten using modern OS X code to better handle long sequences and to provide an OS X look and feel. In addition, you can now display 3 or 6 frame translations below the sequence that update instantly as you edit the sequence.
  • Next Generation Sequencing - The optional add-on assembler module has been enhanced to provide support for next generation sequencing machines. Short read data may be imported in Fastq format and assembled them using the latest version of phrap.
  • Miscellaneous Enhancements - As always, we add a slew of minor enhancements to each release of MacVector designed to improve workflows, speed up processing or provide better integration with the operating system. Look for the ability to change the colors of chromatogram file displays for red/green color blind users, improved import of sequences from Vector NTI and better handling of genomic sequences.

New in MacVector 10.6 (Mar 27, 2009)

  • There is a new function that allows you to directly import sequence data from databases created by Vector NTI Advance v10 or earlier.
  • Select the new Database->Vector NTI Import... menu item and then click on the Choose button to locate the Vector NTI database folder on your file system.
  • The database can reside on a remote Windows machine if required – make sure you share the parental directory containing the Vector NTI Database folder on the remote machine, then connect to that machine using the Finder Go->Connect to Server... menu item.
  • Once a database has been selected, MacVector will display a list of all of the sequences available in the database.
  • There is a popup menu to toggle between Nucleic Acid and Protein sequences.
  • The list can be sorted to more easily identify sequence(s) of interest.
  • Select one or more sequences and then click either the To Desktop button to open those sequences in MacVector, or To Disk to save the sequences in MacVector
  • format to a folder on your hard drive.
  • MacVector will read all of the standard features and annotations associated with each sequence. For this release, feature appearance information is discarded and the default MacVector feature representation are used instead. In addition, MacVector ignores any restriction enzyme sites annotated in the database sequence and replaces them with the default dynamic set of sites used by the Map tab.

New in MacVector 10.5.3 (Mar 16, 2009)

  • Bug Fixes:
  • A number of bugs were inadvertently introduced while adding the exon/frame translation enhancements in 10.5.2. All have now been fixed.
  • The specific bugs were; (a) if you created a protein through a translation, the last two amino acids were always missing; (b) proteins created from minus strand translations were reversed and (c) there were occasional crashes when a result window containing a translation was refreshed (e.g. after changing the Text Display preferences).
  • You can now create “point” features – i.e. features where the start and stop locations are the same residue.
  • The trace file editor has been modified to solve the occasional appearance of extra gaps and to prevent lower case characters from being entered. Also, if the editor has been opened from an Assembly Project, you no longer get unnecessarily prompted to save changes.
  • The name of the second aligned sequence is now correctly displayed in the Pustell Matrix alignment text window.
  • When you “Save As...” a multiple sequence alignment file, the current window now gets its title changed to reflect the new name.

New in MacVector 10.5.2 (Feb 24, 2009)

  • New Functionality:
  • MacVector now honors the standard GenBank /codon_start qualifier to define the start frame of a coding region. This is useful when annotating exons in eukaryotic sequences where the triplet codons may not be in phase due to the presence of introns. Valid values are 1, 2 or 3.
  • The annotated sequence output now correctly displays the translated amino acids for all segmented features in addition to honoring the /codon_start qualifier.
  • Bug Fixes:
  • Several crashes that occurred when saving modified sequences have been fixed.
  • Occasional hangs during startup with the trial version have been resolved.
  • Sequences containing quotes in the annotation comments can now be saved correctly in BSML and Assembly file formats.
  • Junk characters are no longer appended to certain textual result windows.
  • Copying sequence data from a Read feature in the Contig Editor now works correctly.
  • When exiting MacVector with jobs still running, the job manager now waits for your input rather than exiting after 5 seconds.
  • A range selection discrepancy in the Primer3 dialog has been fixed.
  • Selections in the multiple sequence alignment editor now display correctly even when blocking is set to be non-zero.
  • The Results section of the Default Symbols editor dialog now displays the correct labels in the list of results.
  • A “one-out” calculation bug in the pairwise alignment and pairwise matrix result tabs of multiple sequence alignments has been fixed.

New in MacVector 10.5.1 (Jan 13, 2009)

  • A problem where sequence document icons would sometimes be replaced by generic icons was fixed.
  • A crash bug when zooming in the Restriction Enzyme results Map window of large sequences was fixed.
  • Align to Folder now correctly displays the sequence alignments.
  • A crash when importing slightly malformed GenBank files (such as those exported from Vector NTI) has been resolved.
  • A problem where the last line of reports in text windows would be missing has been fixed. This would lead to e.g. the last Restriction.
  • Enzyme not getting reported in the Enzyme Cutters list.

New in MacVector 10.5 (Jan 5, 2009)

  • Long Filenames/File Extensions:
  • The MacVector file reading and writing code has been completely rewritten to fully support OS X conventions. This means that you can now use long filenames (up to 255 characters) and all files are now given suitable extensions so that they can be stored on cross-platform file systems without losing file type information.
  • Universal File Reading:
  • While MacVector has always had the ability to open a wide variety of file formats, in the past certain file import functions could only use a subset of the supported file formats. This limitation has been removed. This affects the following functions;
  • Multiple Sequence Alignment Editor. You can now directly import any valid single or multiple sequence file directly into the editor, ready for alignment by ClustalW. This includes GenBank or EMBL files with multiple entries.
  • Contig Assembly/Align to Reference. You can now directly import any valid single or multiple sequence file directly into the Contig Assembly Project file, or into the Align to Reference editor. Previously you were restricted to MacVector or Chromatogram files.
  • Align to Folder. This function will now scan a test sequence against all valid files in a folder. In particular, you can create databases of many sequences in single files in (e.g.) GenBank, EMBL or FastA format and Align to Folder will search the database for matching sequences. For performance reasons, we recommend you limit the size of any individual file to less than 100MB
  • cDNA Alignments and Splice Site Identification:
  • You can now align cDNA clones against a corresponding genome and MacVector will automatically identify the introns and exons. Actual splice sites at ambiguous junctions are determined using the standard GT..AG intron rule. Once identified you can quickly save each intron or exon as a feature on the parental sequence.
  • Combined Preferences:
  • The various global settings in MacVector have now been combined into a single multiple pane Preferences dialog, accessible from the standard OS X Preferences menu item. This simplifies the configuration of many of the default settings allowing you to customize MacVector to your own personal tastes.
  • Toolbar Customization:
  • The OS X style toolbars introduced in MacVector 10.0 are now fully customizable using the standard OS X editor. You can add, remove and rearrange the toolbar buttons so that you have just the icons you regularly use close at hand.
  • Profile Scans:
  • There is now a simple profile scanning capability built in to the Coding Preference Plot feature, which has been renamed "Nucleic Acid Analysis Toolkit". MacVector reads profile files using the transfac profile format.
  • Licensing Enhancements:
  • If you have purchased more than one MacVector license, you can now have multiple licenses installed on one machine. If the currently selected license is already in use elsewhere on the network, you can quickly toggle to a different license without needing to re-enter the license details.
  • Miscellaneous Enhancements:
  • There is a new Text tab in the Contig Assembly and Align to Reference editors. This displays a simple formatted text view of the alignment that can be printed or copied to other applications.
  • The graphical outputs of the Pustell Matrix analyses, the Protein Analysis Toolkit and the Nucleic Acid Analysis Toolkit (formerly Coding Preference Plot) have been recoded so that they are resized along with the window. This allows the display of large matrices or wide profiles in far greater detail than was possible in MacVector 10.0.

New in MacVector 10.0 (Apr 29, 2008)

  • Licensing Changes - This release of MacVector no longer supports the use of USB Eve3 hardware keys for copy protection. There is a new replacement licensing implementation that ensures that only one copy of MacVector with a given serial number can be running on a network at any one time. All installers now create a temporary license so that you have 30 days to activate the full license.
  • All of the primary windows in MacVector have been rewritten to use OS X-style toolbars. This includes the following windows: Sequence editor, multiple sequence alignment editor, enzyme editor, subsequence editor, map/graphics window, phylogenetic tree window, matrix editor, trace/chromatogram editor, sequence confirmation editor, contig editor and assembly project window. The text and PICT result windows do not use toolbars.
  • To reduce screen clutter and simplify the interface, many of the common windows in MacVector 10.0 have been combined into a single window with tabbed views. For most windows, a �Replica� toolbar button lets you open a second window for those times when you need to see more than one tab at a time.
  • Sequence Window. This now has Editor, Map, Features and Annotations tabs. The corresponding toolbar buttons from the editor window have been removed as they are no longer needed.
  • Trace/Chromatogram Window. This now has Editor, Map, Features and Annotations tabs.
  • Sequence Confirmation Window. This now has Editor, Map, Features and Annotations tabs.
  • Multiple Sequence Alignment Window. The multiple alignment result windows (Text, Pairwise, Matrix, Picture, Guide Tree) have now been added as separate tabs to the main editor window.
  • Contig Window. This now has Editor, Map, Features and Annotations tabs.
  • The feature list has been rewritten to use OS X style lists. This removes the old 8,000 feature limit in earlier versions of MacVector.
  • The feature editor has been completely rewritten to directly support Genbank qualifiers as well as keywords.
  • You can now use the �Find� function to search sequence features based on type and/or text appearing in features or qualifiers.
  • There is a new primer design function in MacVector 10.0. This is based on the popular Primer3 algorithm and is accessed through the Analyze->Primers sub menu.
  • The default Primer3 implementation lets you choose a region to amplify and will automatically find the best 5 pairs of primers. You can also find primers based on product size or by defining flanking regions.
  • There is an option to have Primer3 find a third �Hybridizing Primer� for use in real-time PCR.
  • You can also specify your own primer(s) and have Primer3 evaluate them for suitability.
  • The results are displayed in tabular and graphical format. The views are interactive and linked to the parent sequence so that you can select primers and/or products and copy/paste to other windows or use to create new features on the sequence.
  • You can now have sequences be automatically scanned for restriction enzymes and have these displayed in the default map view. This is configured from the revised Graphic Options dialog, now accessible from a new Preferences button on the Map tab toolbar. By default, this is set to use selected enzymes in the �Common Enzymes� file. This dramatically simplifies the use of MacVector for �click cloning�. You can open a source destination sequence, click on the appropriate restriction sites, choose Edit->Copy to copy the fragment, and paste directly into a matching site in a suitable target sequence.
  • Menu options are no longer disabled when a target sequence is locked. Instead, you are prompted to allow automatic unlocking when you try to invoke a function that would modify the document.
  • You can now save sequence features in a format suitable for use in the NCBI Sequin program for submitting sequences to Genbank. Choose File->Save As� and select the Sequin Feature Table format. There is a new toolbar option in the Sequence Confirmation and Contig Editor windows to display 3 or 6 frame translations underneath the consensus sequence.
  • The Entrez Browser window now supports searching of all available databases at the NCBI, although you can still only directly retrieve sequence entries or PubMed documents. A new preview pane contains a direct web interface to the NCBI web site to view and open non-sequence related links. All downloads now occur as a job in the background, particularly useful as MacVector can now download the large �contig� entries that may contain many MegaBases of sequence.