CodonCode Aligner Version History

Compare CodonCode Aligner version 7.0 with your current version of CodonCode Aligner to see what is new.

 

Feature

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

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 6, 5, 4, 3.5, 3.0, 2.0, 1.6 and 1.5.

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