![]() An improved display of the sample arrows allows the user to get a better idea of gaps and sample position in alignments. The new overview for contigs in CodonCode Aligner was optimized for large projets. On 64-bit versions of Windows, CodonCode Aligner 4.2.1 can now use memory beyond the 1.4 GB limit on 32-bit Windows, up to the available amount of physical memory (RAM). It is comatible with Windows 8 and OS X Mountain Lion (10.8).ĬodonCode Aligner 4.2 introduces support for 64-bit Windows. Such a script can generate dozens of aligned contigs in minutes - a process that may take hours to do in other programs.CodonCode Aligner version 4.0 introduces support for Next Generation Sequencing and several new features and improvements like a new contig overview, building trees for selections, splitting contigs using trees, highlighting sequences with labels, reading and writing new file formats, importing subsets, and much more.ĬodonCode Aligner 4.1 added new filters for the difference table and the option to switch between a stacked and packed overview for aligned samples. Align the resulting contigs to each other with MUSCLE.Align all samples to the reference sequence by name.For example, a script might include the following steps: Scriptingįind yourself doing the same repetive steps over and over? CodonCode Aligner allows you to define scripts for common workflows, and can include scripts you developed in the "Scripts" menu. You can also open a separate table view for your features that can be printed or exported. Once defined, you can use the "Next feature" and "Previous feature" toolbar buttons, or the corresponding keyboard shortcuts, to quickly look at all potential problem regions. Any high-quality discrepancies (for example discrepancies with a Phred quality above 20).Low coverage regions (for example regions that are not covered by at least 2 sequences).Low quality consensus sequence regions (with a threshold you can set).For example, to check a consensus sequence for potential errors, you might define features as any of the following: ![]() In addition to toolbar buttons (and menu items and keyboard shortcuts) to go to the next gap or discrepancy, CodonCode Aligner allows you to define "Regions of Interest" or "Features" for quick navigation. When examining contigs, different users will want to look at different things - for example discrepancies, low quality consensus sequence regions, low coverage regions, or mutation tags. To learn more about customizing toolbars in CodonCode Aligner, have a look at the tutorial movie.įast Navigation: Define What Interests You New users may find buttons with text helpful:Įxperienced users may want to switch to icon-only toolbars to see more buttons, and select the buttons to show: Customizable ToolbarsĮach view in CodonCode Aligner has a customizable toolbar. You can also choose whether to show bases or amino acid translations, how to highlight discrepancies or edited bases, adjust font sizes, window sizes, where new views will be placed, and more. ![]() When looking at contigs, you can quickly mask all bases that match the consensus sequences to focus in on differences: You can also change the colors for each base, and view traceson black background. You can customize how sequences are displayed - colored by base, or using background color to indicate the base, the sequence quality or, or the protein translation. CodonCode Aligner offers many options to customize your workspace so it fits your needs. ![]()
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