![]() License keys for version 5.0 will continue to work with version 5.1.ĬodonCode Aligner 5.1 adds functions to analyze methylation of cytosines after bisulfite modification, PCR, and capillary sequencing. Other customers can purchase an upgrade to version 5. Version 5 is a free upgrade for all users with a current update and support agreement as of March 27, 2014. Please note that CodonCode Aligner 5 requires a new license key. ![]() CodonCode Aligner 5.1.1 introduced methylation analysis and virtual gels. Additional new features include moving multiple gaps with drag & drop, alignments with Clustal Omega, contig overview printing, and multiple speed and memory improvements for large projects and alignments. This version includes several bug fixes and improved methylation analysis accuracy.ĬodonCode Aligner version 5 added functions to create Bowtie2 alignments and display paired end reads. The CodonCode Aligner version history shows a comparison of the features available in different versions.The current version of CodonCode Aligner is 5.1.5. What is new in CodonCode Aligner version 3.0. ![]() The new features and improvements listed above describe Watch the movie for a demonstration of the new features. Paste text sequences directly into the base.Quality scores due to a KB basecalller bug) now works better. Importing contigs from FASTA (and similar) files.Īssemblies, contigs are now sorted by the number of samples theyĬlipping for sequences that contain many Ns (with unreasonably high Remove leading and trailing contig gaps atĪre removed automatically from the start and end of sequences when.How much memory CodonCode Aligner uses directly in the project view. View: Wondering if you can add more sequences to you Automatic memory handling on Windows: CodonCodeĪs is needed and available (up to 1.4 GB), without the need to edit.To allow import of aligned contigs in other programs. Add gaps at the start and end of sequences in contigs, Append the number of sequences in contigs to the file.Īppend comments. More control when exporting in FASTA format:Ĭontrol the replacement of spaces or other.Import 454ĭata from SFF files, and assemble by multiplex ID tags.Īssemblies on a test data set. Substantially faster when working with thousands of samples. Assembly and alignment has been optimized to be Reduced memory use allows you to work with 3 x Genbank or FASTA from the clipboard to create single or mutiple new CodonCode Aligner automatically parses known formats like Choose to run a script when starting CodonCode Aligner orĪccess your scripts quickly through the new script menu.Įasily create new text sequences using copy and New script commands make scripting in CodonCode Aligner better thanĮver. Use scripts to facilitate your daily work. Hundreds of sequences into your CodonCode Aligner project. ![]() Specify multiple sequences or ranges to import Import sequences directly from GenBank byĪccession number. Switchīetween compact size for overviews and a larger size for details. Use differentįilters to control what to display in your Difference Tables. Simply by clicking on any cell in the difference table. With chromatograms, or when looking at base views.Įasily spot the differences in your contigs by Quickly change the readingįrame by toolbar button or menu. Independent from the background, select to see the bases or theĪmino acid translation for your sequences. Choose between translation-basedīackground colors, colored nucleotides, or quality-based backgroundĬolors. Simply switch between showing bases and amino acid ![]()
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