What's new in CodonCode Aligner 7.1.2
Aug 28, 2017
- Fixes a bug that caused changes to alignment and assembly preferences to not be saved.
New in CodonCode Aligner 7.1.1 (Jul 25, 2017)
- Adds support for adapter removal and trimming of NGS reads with BBDuk2; a new option for NGS assemblies using the program Tadpole; faster NGS assemblies when using the CodonCode NGS assembly algorithm; and improved assemblies of NGS projects with very high (>200x) coverage. This version also fixes a number of minor bugs. All users of CodonCode Aligner version 7.0.1 should upgrades to this version. License keys for version 7.0.1 will continue to work with this version.
New in CodonCode Aligner 7.0.1 (Feb 17, 2017)
- "Under the hood" changes that have been requested by customers and improve performance. On OS X, CodonCode Aligner now contains a "bundled" JRE, and does not require the separate installation of an outdated Java version anymore. This required that support for OS X 10.6 was dropped.
New in CodonCode Aligner 6.0.2 (Oct 22, 2015)
- Fixes bugs introduced in version 6.0.1.
New in CodonCode Aligner 6.0.1 (Oct 22, 2015)
- Primer Design:
- Primer design in CodonCode Aligner 6 utilizes Primer3 to pick sequencing or PCR primers. Primer can be imported in the current project and are highlighted in the template sequence.
- Create primer pairs for PCR at the optimal location within a setable range surrounding the target, cloning primers at a fixed location, or sequencing primers in an adjustable interval.
- Primer picking parameters are highly adjustable and primer features can also be accessed after import.
- For ordering, primers can be exported in csv file format which is commonly used.
- Bacterial Genome Assembly:
- Aligner 6 add the option to create fast and memory efficient bacterial genome assemblies.
- Aligner's scaffolding algorithm generates accurate scaffolds with high coverage.
New in CodonCode Aligner 5.1.5 (Feb 3, 2015)
- This version fixes several bugs, and offers improved accuracy in methylation analysis.
New in CodonCode Aligner 5.1.4 (Dec 10, 2014)
- This version fixes several bugs, and offers improved end overlap detection when assembling large contigs.
New in CodonCode Aligner 5.1.3 (Nov 24, 2014)
- The web address for BLAST searches has been updated to reflect changes made by the NCBI.
New in CodonCode Aligner 5.1.2 (Nov 18, 2014)
- Adds improved accuracy in methylation analysis from bisulfite ABI data, and fixes a problem where double-clicking on CodonCode Aligner projects in Windows resulted in an error dialog.
- Bug fixes and improvements:
- Double-clicking on Aligner project files on Windows works again
- Improved methylation analysis accuracy by subtracting background
- Changed format for methylation analysis tags to show background subtracted
New in CodonCode Aligner 5.1.1 (Nov 4, 2014)
- New Features and Improvements:
- New "virtual gel" view for restriction maps
- Support for methylation using ABI chromatograms
- New function to convert Cs to Ts in Edit -> Change bases
- In trace views, trace values can now be displayed by hovering with the mouse and pressing the "Shift" key
- New "setComments" script command to change comments for current selection
- Adapted to Mac OS X 10.10 (eliminated misleading error message)
New in CodonCode Aligner 5.0.2 (Jun 7, 2014)
- Fixes several bugs, and adds improved amino acid translations for codons with ambiguitues.
New in CodonCode Aligner 5.0.1 (Mar 28, 2014)
- Adds many new features:
- Support for alignments with Bowtie2
- The option to display paired ends for Bowtie2 alignments in the contig view
- Support for Clustal Omega
- Improved gap editing, contig overview printing, and multiple speed and memory improvements for large projects.
New in CodonCode Aligner 4.2.7 (Feb 4, 2014)
- Contains several important bug fixes, including a workaround for problems setting the memory for CodonCode Aligner on OS X 10.9.1.
New in CodonCode Aligner 4.2.5 (Dec 4, 2013)
- This version fixes a problem saving large projects that could occur in certain rare situations. All users of CodonCode Aligner version 4.0.1-4.2.4 should update to this version.
New in CodonCode Aligner 4.2.4 (Sep 23, 2013)
- Fixes a crash on some Windows computers.
New in CodonCode Aligner 4.2.3 (Sep 3, 2013)
- Fixes a potential hang when opening files, and includes improvements and bug fixes related to importing files in SAM format.
New in CodonCode Aligner 4.2.2 (Jul 22, 2013)
- This version fixes several bugs related to importing files in SAM and FASTQ format.
New in CodonCode Aligner 4.1.1 (Mar 2, 2013)
- New difference table filters and a "stacked" overview layout option, as well as a number of bug fixes and improvements.
New in CodonCode Aligner 4.0.4 (Aug 13, 2012)
- Includes several important bug fixes; all users of CodonCode Aligner version 4.0.1-4.0.3 should update to this version.
New in CodonCode Aligner 4.0.3 (Jun 7, 2012)
- Includes several bug fixes and minor improvements, including the ability to export "unformatted" FASTA files (all bases for a sequence are on a single line).
New in CodonCode Aligner 3.7.1 (Sep 22, 2010)
- New Features and Improvements:
- Gaps ('-') in consensus sequences can now replaced with 'n' to preserve gaps in contigs when comparing contigs with MUSCLE
- When comparing contigs with MUSCLE and contigs contain gaps, a warning dialog that the gaps may be deleted will be shown (once per session)
- Changes:
- When comparing contigs that were created by aligning to a reference sequence with MUSCLE, CodonCode Aligner no longer includes copies of the reference sequence in the alignment, as older version did to minimize deletion of gaps
- Bug fixes:
- Fixed a problem where "Compare Contigs" with MUSCLE sometimes failed
- When showing translations for contigs with many gaps, redrawing occasionally failed, which caused screen artifacts and/or apparent hangs - fixed
- Addressed a problem where extended licenses sometimes became unusable with an "Invalid computer ID" message on Windows
- Deleting bases in contigs of contigs ignored the fill direction - fixed
- When inserting gaps in contigs, settings to mask the consensus were ignored - fixed
- Assembling or aligning several large sequences with the large gap algorithm sometimes was very slow, and canceling did not work properly - fixed
- Other minor bug fixes
New in CodonCode Aligner 3.6.1 (Jul 31, 2010)
- New Features and Improvements:
- New "Make Lower Case" and "Make Upper Case" functions in the "Edit" menu
- Contig tags and comments are now preserved when samples are added to existing contigs
- The various "Change Bases" auto-edit functions can now be accessed through a sub-menu in the "Edit" menu
- Bug fixes:
- Fixed a bug that sometimes caused error dialogs to be shown after editing
New in CodonCode Aligner 3.5.7 (Jun 15, 2010)
- Bug fixes:
- Low memory problems when aligning with Muscle or Clustal could lead to data loss fixed
- Fixed a problem where Neighbor-joining trees were incorrect when masking bases
- that match the consensus was used
- When navigating through contigs of contigs with "Auto-select traces" selected,
- trace views are now properly updated to show the currently selected sub-contig
- Fixed a problem where trace views were sometimes not drawn properly when displaying
- translations or translation-based backgrounds
- When changing selections in trace views, the contig view would sometimes become the
- active window fixed
- Unassembling alignments to reference sequences with coding sequence annotations
- sometimes result in errors related to codonStart tags fixed
- Error dialogs where sometimes shown after creating a new text sequence fixed
- Fixed a problem where sample and contig dates where incorrect when opening
- projects with contigs of contigs
- After using "Go to base", shift-click selections selected the wrong bases fixed
- Fixed a problem where consensus tags were sometimes moved to wrong positions
- when using "Split contig"
- Changes:
- Difference tables now always use a "by base" color scheme when shown condensed
- On Mac OS X, the "Import sample" file dialog has been improved
New in CodonCode Aligner 3.5.6 (Apr 5, 2010)
- Improvements:
- Several substantial improvements for very large difference tables:
- faster scrolling
- faster application of filters
- contigs views with large difference tables now open right away
- when exporting tables with many (>256) columns, rows and columns are now transposed to enable import into spreadsheets
- Bug fixes:
- Fixed a Windows-specific problem where Aligner would sometimes quit after computer sleep (standby or hibernation)
- When creating new text sequences, selecting "Use clipboard" would overwrite a previously entered name - fixed
New in CodonCode Aligner 3.5.5 (Mar 19, 2010)
- Quit CodonCode Aligner if Aligner is running.
- Download the installer for CodonCode Aligner 3.5.5 using the links above
- Install the new version at the same location as the previous version (typically in /Applications).
New in CodonCode Aligner 3.5.4 (Feb 22, 2010)
- Quit CodonCode Aligner if Aligner is running.
- Download the installer for CodonCode Aligner 3.5.4 using the links above
- Install the new version at the same location as the previous version (typically in /Applications).
New in CodonCode Aligner 3.5.3 (Feb 3, 2010)
- Quit CodonCode Aligner if Aligner is running.
- Download the installer for CodonCode Aligner 3.5.3 using the links above
- Install the new version at the same location as the previous version (typically in /Applications).
New in CodonCode Aligner 3.5.2 (Jan 6, 2010)
- New Features and Improvements:
- Selecting long regions (thousands of bases) is now substantially faster
- Reduced memory use when working with long text sequences
- Bug fixes:
- Creating phylogenetics trees for alignments to reference sequences sometimes failed - fixed.
- Fixed minor tree drawing problems.
New in CodonCode Aligner 3.0.3 (Jul 9, 2009)
- Amino acid translation for all samples.
- Protein translation based background colors.
- Difference tables.
- Import directly from GenBank.
- Script menu.
- New script commands.
- Import 454 data (SFF files).
- Create new text sequences.
- Support larger projects.
- Faster assemblies.
- Automatic memory use on Windows.
- Improved pen tablet support.