What's new in Sequencher 5.4.6
Nov 10, 2016
- New and enhanced features for all of your DNA sequence analysis.
- Sanger:
- Send primer pair sequences from Primer-BLAST runs in Sequencher Connections to your Sequencher project.
- Easily use consensus sequences from the Project Window as a reference sequence for NGS alignments for hybrid sequencing projects.
- New Batch Revert Trim Ends command.
- Ability to adjust the font size in the Project Window.
- NGS:
- Faster GSNAP and BWA-MEM workflows.
- Build GSNAP Databases and BWA Indexes that can be re-used for aligning to whole genomes.
- View and save quality scores and metadata of your NGS raw data files with FastQC reports.
- Generate Variant Calling Files (VCF) to flag variants in your NGS alignments using SAMtools.
- RNA-Seq:
- Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm.
- A unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
- Enhanced RNA-Seq visualizations with custom sorting and filtering options.
- Easily manage all of your DNA-Seq and RNA-Seq projects with an enhanced External Data Browser.
New in Sequencher 5.4.1 (Jan 18, 2016)
- Adds features to Sanger and NGS such as:
- Build GSNAP Databases and BWA Indexes that can be re-used and persisted with your project.
- Sequencher is able to handle larger genomes when aligning sequences using GSNAP and BWA.
- An updated External Data Browser that now includes a Final Run Status column that will report statuses of SUCCESS and FAILED.
- An updated External Data Browser that includes run results for new DNA-Seq options for GSNAP Databases and BWA Indexes.
- Sequencher Connections now offers the ability to send primer pair sequences returned from a Primer-BLAST run to your Sequencher project.
- Primer sequences sent to your Sequencher project from Sequencher Connections have colored bases and primer features applied to them.
New in Sequencher 5.4 (Nov 18, 2015)
- This new release adds features to Sanger, NGS and RNA-Seq analyses such as:
- Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm. Sequencher 5.4 also has replicates functionality with a unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
- Enhanced RNA-Seq visualizations with custom sorting and filtering options.
- View and save quality scores and metadata of your NGS raw data files with FastQC reports.
- Generate Variant Calling Files (VCF) to flag variants in your NGS alignments using SAMtools.
- Updated version of GSNAP which runs faster and has additional alignment modes.
- An updated External Data Browser for organizing both DNA-Seq and RNA-Seq projects.
- Sequencher Connections has improved organization and usability.
New in Sequencher 5.3 (Dec 22, 2014)
- Introduces new functionality for RNA-Seq analyses, as well as enhancements to Sequencher Connections.
New in Sequencher 5.2.4 (Sep 29, 2014)
- Combines support for all licensing options whether it's standalone or network, dongle or keyless.
- Network customers using KeyServer now have access to all the latest features:
- Sequencher Connections - A whole new way to accelerate your analysis! Perform multiple customized BLAST searches or MUSCLE alignment on single or groups of sequences. View your results in webpage, text, or XML format all without leaving Sequencher!
- Use MUSCLE to create phylogenetic trees that can be viewed in multiple formats.
- BWA reference-guided alignment algorithm for NGS data sets.
- Added GSNAP flexibility - You now have the ability to capture reads that didn't align, or even to select only reads that didn't align.
New in Sequencher 5.1 (Nov 26, 2012)
- New features include:
- De Novo Alignment for NGS data
- Multiplex ID Assembly
- A new sequence alignment algorithm for Sanger data
- A protein searching feature for any type of DNA sequence data
New in Sequencher 5.0.1 (Jan 6, 2012)
- What’s New:
- Lion Compatible Sequencher is now Intel-native and runs on all version of MacOS X from 10.5 to 10.7.
- Longer Reference Sequences Sequencher can now handle reference-guided alignments of over 200 million bases.
- Enzymes from ReBase now supported With this release of Sequencher you now get the ReBase commercial enzyme list.
- KeyServer Notifications If all network licenses are out you will now be notified and placed in a queue for the next available if you wish.
- What’s Improved or Changed:
- Performance There have been improvements in performance throughout Sequencher.
- Default Save Path The default Save Project path is now to the Sample Data folder in Sequencher’s application folder.
- Last location remembered for Open, Save and Import Folder Commands The Sequencher Open, Save and Import Folder of Sequences commands now remembers the last folder used.
- Missing Templates If a Template is missing Sequencher now creates a new blank project and resets the template project preference to
- New Blank Project.
- ACE Projects and long sequence names You can now import ACE and CAF projects with internal names longer than 31 characters.
New in Sequencher 4.10.1 (Mar 24, 2010)
- New:
- Option to Compute Consensus by Confidence - There is a new method that can be chosen for computing the bases that make up the consensus string. Consensus by
- Confidence uses the base with the highest confidence score in the column to use as the consensus base. -
- Consensus line shows confidence shading - When Consensus by Confidence is used, the consensus line can show confidence shading.
- “Create New Sequence from Consensus” includes consensus confidence scores - This is only applicable if you have computed the consensus using the By Confidence method.
- Contig Coverage Graph - A new version of the Overview shows the depth of forward and reverse coverage as a histogram.
- Generate a Shuffled sequence - With this new command, bases of a chosen sequence are randomized to create a new sequence with the same composition
- but a different order.
- Frequency Histograms and Tables - Nucleotide frequency information is now available as a report. You can generate tables or a histogram.
- New Import Formats - Three major formats have been added to the extensive set currently available. These are FastQ, FastA aligned, and Contig Express projects.
- Support for Contig Express project files (the assembler from VectorNTI) - For those of you who have legacy projects assembled with ContigExpress (file extension .cep), you can import those projects into Sequencher, including sequence bases, names, contigs, electropherograms, features, confidence scores, base edits (including insertions and deletions), and comments.
- Consensus by Confidence in the Variance Table - When the Compare Consensus to Reference command is used, you see Confidence Range colors in the cells of the table
- where there are variant bases.
- New Difference Column in the Variance Table - A new column containing the total number of differences has been added to a number of the Variance Table reports.
- Sort by Handle - A new option to sort “by Handle” has been added to the Contig Editor Overview.
- New AppleScript commands Get and Retrieve project item values - New AppleScript commands have been added to Get and Set labels and comments on any fragment, contig, or refrigerator in
- the Project Window. Comments on the Project can also be accessed through Get and Set commands in AppleScript.
- New AppleScript commands to access whether an item is Selected - New AppleScript commands have been added to Get and Set the Selection state of an item.
- What’s Improved:
- Multiple Feature Listings - The ability to open the Feature Listing has been extended from one sequence to a number of sequences at the same time.
- Chromatograms on the Variance Detail Report -It is now possible to set the scaling of chromatograms in the Variance Detail report.
- Scroll Wheel enabled in more dialogues - The Scroll Wheel on a mouse now allows you to scroll vertically through the lists in the “Assemble Interactively” dialogue.
- Sort Project Windows by column - Project Window columns may now be sorted in an ascending or descending order for any column.
- Improved support for file extensions on Apple’s “Snow Leopard” operating system - We addressed the change that Apple Computer introduced so that all the correct file types are visible in the Open Project dialog, including files ending with .spf, .SPF, .Spr and those with allowed Apple “TYPE” and “Creator” codes.
- Trim Log File - There is a new command to assist you in navigating to and opening the log file.
- More “Don’t Show Again” checkboxes - At the request of users, more warning dialogues have been given a “Don’t show this message again” checkbox.
- Sequence trimming is much faster - Ends trimming and vector trimming are now substantially faster operations, especially on large data sets.
- Improved “Snow Leopard” compatibility (Macintosh) - We addressed changes that Apple Computer made which affected file type recognition as well as a change that affected
- Clustal.
- Improved File Lists on Macintosh - We addressed an issue so that ACE and CAF files are now enabled and selectable in the file lists when importing ACE and CAF
- projects.
- In Assemble by Name, more room for Advanced Expression - The Advanced Expression type-in box has been made wider to accommodate longer advanced expressions for complex
- naming conventions.
- Unusable characters in file names are detected on Windows - We catch and handle a problem that was seen primarily on non-English systems on Windows. Unrecognizable characters in
- the full path name of a file are detected and tell you what needs to be changed for import or export.
- “Lost” user preferences have been fixed - An issue has been fixed where some of the User Preferences could get lost. One manifestation of this was that you might get asked to register your copy of Sequencher over and over again.
- % Quality for Contigs - A contig will have a % Quality value when Consensus by Confidence is in use.
- Increased number of bases trimmed in Vector contamination - The limit of bases trimmed in Vector contamination has been increased to 99 at each end.
New in Sequencher 4.9 (Apr 2, 2009)
- What’s New:
- Translated Variance Table – The Translated Variance Table summarizes all amino acid differences in a selected set of samples. Because the table is linked to the underlying sequence data, it is ideal for validating mutations that result in changes to the amino acid translation and for checking expression vectors.
- Filter the Results of the Variance Tables – You can restrict your Variance Table to just coding sequence, or just variants, or exons, or genes, or any region specified with a feature. Similarly you can define a Translation Range, even across multiple introns, for the Translated Variance Table.
- Reports – Sequencher’s new reporting creates printable versions of your data. The Reports provide analysis tools such as clustering of like samples in the Population Report and calculating the percentage of secondary peak heights in the Variance Detail Report.
- SuperPro Key support – We replaced the purple Eve3 key with the fully supported blue or black and blue SuperPro key. This change increases the compatibility of Macintosh standalone licenses on newer Macintosh operating systems.
- What’s Improved:
- Improved Sequence Features – Sequencher now imports GenBank features with complex locations, such as the joined and ordered locations that are common in exon and mRNA features. Sequencher also has improved tools for the import and annotation of complemented features.
- Enhancements to the Variance Table – We have added more tools to enhance the utility of the Variance Table. From column selections you can now label, add comments to, and get info from samples. You can also selectively remove columns from the table as you work.
- Better Translation Tools – The Reference translation now updates as you edit, and a new option forces the frame of the consensus translation to correspond to the Reference. Sequence Editors will now translate joined features even when they are separated by non-coding sequence.
- Contextual Menus – You can invoke context-sensitive menus in some Sequencher windows by using the right-mouse click on Windows and right-mouse click or Ctrl+click on Mac.
New in Sequencher 4.8 (Jun 6, 2008)
- What�s New
- Translated Variance Table � The Translated Variance Table summarizes all amino acid differences in a selected set of samples. Because the table is linked to the underlying sequence data, it is ideal for validating mutations that result in changes to the amino acid translation and for checking expression vectors.
- Filter the Results of the Variance Tables � You can restrict your Variance Table to just coding sequence, or just variants, or exons, or genes, or any region specified with a feature. Similarly you can define a Translation Range, even across multiple introns, for the Translated Variance Table.
- Reports � Sequencher�s new reporting creates printable versions of your data. The Reports provide analysis tools such as clustering of like samples in the Population Report and calculating the percentage of secondary peak heights in the Variance Detail Report.
- SuperPro Key support � We replaced the purple Eve3 key with the fully supported blue or black and blue SuperPro key. This change increases the compatibility of Macintosh standalone licenses on newer Macintosh operating systems.
- What�s Improved
- Improved Sequence Features � Sequencher now imports GenBank features with complex locations, such as the joined and ordered locations that are common in exon and mRNA features. Sequencher also has improved tools for the import and annotation of complemented features.
- Enhancements to the Variance Table � We have added more tools to enhance the utility of the Variance Table. From column selections you can now label, add comments to, and get info from samples. You can also selectively remove columns from the table as you work.
- Better Translation Tools � The Reference translation now updates as you edit, and a new option forces the frame of the consensus translation to correspond to the Reference. Sequence Editors will now translate joined features even when they are separated by non-coding sequence.
- Contextual Menus � You can invoke context-sensitive menus in some Sequencher windows by using the right-mouse click on Windows and right-mouse click or Ctrl click on Mac.