Version 1.5

New in CodonCode Aligner Version 1.5

This page describes the most important changes and new features in CodonCode Aligner version 1.5. Please read about features in CodonCode Aligner version 1.6 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 build 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:

the option to automatically group samples by their names, and to assemble each group separately (described above)
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
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.

Old news: New in CodonCode Aligner Version 1.4.6

This page describes the most important changes and new features in CodonCode Aligner version 1.4. All of these new features have been requested by users - thanks to all who have given us feedback. Changes include features to organize, find, and rename sequences; improvements in mutation detection; and other features like speed improvements and user-defined locations for the preference file.

This release is a free update to all CodonCode Aligner customers.

Version 1.4.5 fixed a number of bugs, including problems when saving and re-opening some problems.
Version 1.4.6 fixed a bug when using the "Assemble with Phrap" option that was introduced in version 1.4.5. All users should update to version 1.4.6.

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

Organizing and Finding Sequences

Manual folders: You can now create folders in the project view to organize unassembled sequences.
Icons for alignments: Alignments to reference sequences now have icons that are different from assembled contigs, making it easy to see whether a contig is an alignment or an assembly.
Find by name: You can search for sequences by name in the project view, contig view, and trace view.
Easy renaming: Sequences and contigs can now be renamed directly in the contig view. Names can contain spaces, accented characters, etc.

The following screen shot illustrates these features:

New & Improved Mutation Detection Features

Multiple reference sequences: A project can now have multiple reference sequences, which can be different or identical.
Better Genbank file reading: When reading sequences from text files in Genbank format, Aligner will now parse all coding sequence ("CDS") tags as well as "variation" tags that describe known mutations.
Fast editing of false positives: False positive heterozyous point mutations can now quickly be marked as "false positives" from popup menus or the corresponding keyboard shortcut.
Mutation tables now are updated when you edit mutations
Protein translations for coding regions: For alignments or contigs with defined coding regions, the protein translation for the defined coding region(s) can be shown.
Improved heterozygous indel detection: The sensitivity and accuracy of heterozygous indel detection has been improved substantially.
Improved heterozygous indel analysis: CodonCode Aligner version 1.4 now offers two seperate methods to analyse heterozygous indels - trace subtraction and second peak analysis. The "second peaks analysis" methods can give sequence estimates for heterozygous indels even if no reference chromatograms are available. Trace subtraction has been optimized to give better results if the sequence from the mutated allele is weaker than the non-mutated sequence.

The screen shot below shows an example of the new indel processing:

In the sample at the top ("indel"), the base calls have been replaced by the deducted sequence of the second allele. The sequence in the middle ("indel_sub") is the artificial sequence created by subtracting a scaled reference trace (shown at the bottom) from the indel trace. Note that both algorithm give the same sequence, which has a 5 base deletion.

Other New Features and Improvements

Speed improvements: Project opening, alignments to large reference sequences, and scrolling in contig views and trace views is faster.
Bug fixes: Many bugs in older versions of CodonCode Aligner have been fixed.
View synchronization: Moving in one view will now correctly move to the corresponding position in other open views (if the sequence is shown in other views)
Trace views: The width of trace view windows is now remembered and used when opening new trace views.
Custom preferences: Users can now define the location of preference files, for example to use shared preferences for work groups from a network disk. Preference files can also be "locked" by not writing any changes back to the preferences.
Contig view printing: The protein translation is now included when the contig view is printed.
Double-clicking on text sequences: When double-clicking on sequences that do not have chromatograms, a base view window is opened.
Better gap placement: The alignment and assembly methods now use separate gap initiation and extension penalties, which typically leads to better placement of gaps.

The screen shots below show the improvements in gap placement. The first image shows the placement of gaps with CodonCode Aligner version 1.4.0 beta 3:

The image below shows the gap placement with CodonCode Aligner 1.3.4:

Clearly, the use of separate "gap initiation" penalties results in much better placement of gaps.

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

CodonCode Aligner

Phred

Phrap

Consed

PolyPhred

TraceViewer