New in CodonCode Aligner Version 1.5

This page describes the most important changes and new features that were introduced in CodonCode Aligner version 1.5. Please read about features in the current version of CodonCode Aligner on a separate page.

All of these new features have been requested by users - thanks to all who have given us feedback.

  • Assembly by group: To quickly assemble multiple contigs, for example from different species or patients, you can define how Aligner should interpret sample names to automatically group samples. Aligner can then automatically assemble samples in each group separately. A Flash tutorial is available.
  • Compare contigs: CodonCode Aligner version 1.5 lets you compare a set of contigs by building "contigs of contigs", for example for phylogenetic studies. To verify differences between contigs, double-clicking in the "contig of contigs" will show the original traces. A Flash tutorial is available.
  • One-step processing: You now have the option to do base calling, end clipping, vector trimming, and contig assembly in a single step.
  • BLAST searches: Database comparisons with BLAST can now be initiated directly from CodonCode Aligner. A Flash tutorial is available.
  • Improved exporting: Aligner now offers additional export formats for phylogenetic programs, including Phylip and NEXUS/PAUP. Aligner will warn about potential problems that may arise from long file names etc., and offer to automatically fix such problems in the exported files.
    In addition, you can now export translated protein sequences.


If you are still using CodonCode Aligner version 1.3.9 or older, please also read about the changes introduced in CodonCode Aligner version 1.4.

Assemble by groups

If your projects contain many contigs, for example from different species or patients, the new "Assembly by groups" option can greatly simplify your life. In CodonCode Aligner 1.5, you can:

  • define different parts of sample names that can be used to group samples
  • let Aligner automatically assemble your sequences into separate contigs for each group of samples

To quickly find and verify differences between these contigs, you can compare contigs, as defined in the next section.

Compare contigs

CodonCode Aligner allows you to build "contigs of contigs" - to align consensus sequences from different contigs, and to quickly go back to the original sequence traces by double-clicking in the original sequence traces. Typical uses of this functions include:

  • Phylogenetic analysis of sequence changes between different species
  • Population genetic studies of different geographic isolates
  • Comparison of viral gene sequences for isolates from different patients

CodonCode Aligner version 1.5 offers two new features that greatly simplify this task:

  1. the option to automatically group samples by their names, and to assemble each group separately (described above)
  2. the option to compare contigs to each other by building "contigs of contigs".

Both options can be accessed through the "Assemble with Options..." item in the "Contig" menu.

One step processing

Another time-saving feature in CodonCode Aligner 1.5 is the option to automatically pre-process samples before assembly. For any unassembled samples, Aligner can automatically do the following steps:

  • Call bases and assign quality scores with PHRED (for sample that do not have base-specific qualities)
  • Find heterozygous insertions and deletions
  • Clip ends to remove low-quality sequence from the start and end
  • Trim vector sequences.

Any combination of these options is available in the "Preprocessing" pane of the "Assemble with options" dialog:

BLAST searches

CodonCode Aligner version 1.5 now allows you to start BLAST searches directly from Aligner. Just select the sequence you want to BLAST in any of the Aligner windows, and choose the desired BLAST search option from the "Go" menu. Aligner will open the correct NCBI BLAST page, and past your sequence into the search field. Searching multiple sequences with MegaBLAST is also supported.

Improved exporting

For further editing and analysis with commonly used phylogenetics program, version 1.5 of CodonCode Aligner offers improved exporting of contigs in NEXUS/PAUP and Phylip formats. Since some phylogenetic analysis programs can be rather picky about file format, Aligner support both sequential and interleaved formats. In addition, Aligner offers options to convert names that may cause problems in some programs automatically, for example by shortening long names and replacing problem characters like spaces.

Other new features and changes

The previous menu items "Assemble from scratch" and "Assemble with PHRAP" have been dropped, and these functions are now available through the "Assemble with Options" dialog. The "Assemble with Options" dialog provides explanations for the various assembly options, which have sometimes confused new users.

For projects with large numbers of contigs, CodonCode Aligner 1.5 now lets you organize samples and contigs in folders. For example, you can create folders for contigs in different states of analysis, and simply drag and drop contigs in the contig view from one folder to the next when an analysis step is completed.

CodonCode Aligner version 1.5 also includes a large number of optimizations and bug fixes; we strongly recommend that all users of older versions update to the most recent version.

Please note that this page is does not describe the most recent new features in CodonCode Aligner - the newest changes are described here.

Copyright © 2013 CodonCode Corporation. All Rights Reserved.