CodonCode Aligner Version History

Compare CodonCode Aligner version 8.0 with your current version of CodonCode Aligner to see what is new.



v 1.5

v 1.6

v 2.0

v 3.0

v 3.5

v 4.0

v 5.0

v 6.0

v 7.0

v 8.0

Amino acid based alignments


Cluster sequences (NGS / metagenomics)


Identify sequences (NGS / metagenomics)


Dot plots


NGS trimming and adapter removal with Bbduk2


NGS assembly with Tadpole


RFLP analysis


New algorithm for bacterial NGS assembly


Improved scaffolding


Better performance on 64-bit Windows


Primer design


Assemble bacterial genomes


Methylation analysis


Virtual gel


Align with Bowtie2


Show paired ends in contig overview


Create alignments with Clustal Omega


Move multiple gaps with drag&drop in contig view


Remove consensus gaps


Support for 64-bit Windows


Stacked and packed contig overview


Additional difference table filters


Contig overview printing


Speed improvements for large projects


Memory improvements for large projects


Show colored discrepancies in sample arrows


Display coverage with colored differences


Zooming for sample arrows in contig view


Import a subset of sequences


Build tree for selected bases only


Split contig by tree


Highlight sequences with labels


Read & write fastq files


Read sam files


Add tags to all samples at the same time


Support for larger projects


Faster assemblies & alignments


Make sequences upper / lower case


Replace gaps ('-') in consensus sequences


Neighbor-Joining trees


Percentage consensus


Contig view zooming for bases


Automatic ref. 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


For more details about those features, please look at the new feature descriptions of version 7, 6, 5, 4, 3.5, 3.0, 2.0, 1.6 and 1.5.

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