CodonCode Aligner Version History

Feature

v1.5 (2006)

v1.6 (2006)

v2.0 (2007)

v3.0 (2009)

v3.5 (2009)

Neighbor-Joining trees

Percentage consensus

Contig view zooming

Automatic reference seq. shortening after alignment

Mask bases with low coverage

Set base numbers

Customize toolbars through popup

Automatic name scheme definition

Speed improvements for many contigs

Rebuild consensus

Support for bi-directional scrolling

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

Restriction maps

Align to reference in groups (by name)

Create sequence alignments with muscle

New consensus options

Automatically edit to match consensus sequence

Call secondary peaks

Change ambiguities to bases

Convert low quality bases to N

Print preview for all views

Split indels in pseudo-allels

Trace sharpening

Support scripting

Export unphased haplotypes

Improved mutation analysis

Large gap (cDNA to genomic) alignments

End-to-end assemblies & alignments

Improved detection of heterozygous indels

License Server support

Support NBRF/PIR format

Drag & drop folders on project view

Roundtrip editing

Contigs of contigs (align contigs)

Create alignments with ClustalW

Assemble in groups (by name)

One-step processing

Start BLAST searches

Mask bases matching the consensus sequence

Export protein translations