CodonCode Aligner introduced several features and improvements like building Neighbor-Joining trees, zooming in the contig view, shortening reference sequences after alignments, masking contig bases in low coverage regions, the percentange consensus as additional consensus method, and much more.
With CodonCode Aligner, you can:
* Import sequences from text files
* Import sequences from ABI and SCF files
* End clip
* Vector trim
* Assemble contigs
* Align to a reference sequence
* Align contigs to each other while keeping the links to the traces
* Assemble or align in groups, based on sample names
* Find heterozygous mutations
* Analyze heterozygous insertions and deletions
* Define regions of interest ("features"), for example low quality consensus regions
* Quickly navigate between user-defined features
* Import and edit Phrap-generated assemblies
* Run Phred and Phrap directly from Aligner projects
* Export sequences and features
* Export Consed-compatible assembly projects
CodonCode Aligner lets you take full advantage of modern algorithms for base calling and sequence assembly, without forcing you to learn complicated command line options or Perl programming.
Creates a high number of bioinformatics analyses, with graphical shown results.
Comments (2)