CodonCode Aligner Version History

TA cloning

TOPO cloning

Blunt-end (PCR & TOPO) cloning

Transfer features between sequences

See features in contig overview

Gibson Assembly

Find common features

Synchronize starts

Import GFF files

Open recent files

Set start in circular sequence

Improved alignments for circular sequences

Restriction cloning

Separate alleles

Sequence maps

Show start and stop codons for samples

Single letter amino acid translations for samples

Display features and enzymes in base view

Export in Genbank and EMBL format

Import all features from EMBL and Genbank files

Select samples by length, name, direction, sequence

Select range of bases

Change tag colors

Improved clustering speed and accuracy

Amino acid based alignments

Cluster sequences (NGS / meta genomics)

Identify sequences (NGS / meta genomics)

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