CodonCode Aligner Version History
Compare CodonCode Aligner version 10.0 with your current version of CodonCode Aligner to see what is new.
Feature |
1.5 |
1.6 |
2.0 |
3.0 |
3.5 |
4.0 |
5.0 |
6.0 |
7.0 |
8.0 |
9.0 |
10 |
Restriction cloning |
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Separate alleles |
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Sequence maps |
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Show start and stop codons for samples |
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Single letter amino acid translations for samples |
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Display features and enzymes in base view |
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Export in Genbank and EMBL format |
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Import all features from EMBL and Genbank files |
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Select samples by length, name, direction, sequence |
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Select range of bases |
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Change tag colors |
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Improved clustering speed and accuracy |
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Amino acid based alignments |
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Cluster sequences (NGS / metagenomics) |
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Identify sequences (NGS / metagenomics) |
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Dot plots |
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NGS trimming and adapter removal with Bbduk2 |
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NGS assembly with Tadpole |
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RFLP analysis |
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New algorithm for bacterial NGS assembly |
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Improved scaffolding |
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Better performance on 64-bit Windows |
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Primer design |
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Assemble bacterial genomes |
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Methylation analysis |
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Virtual gel |
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Align with Bowtie2 |
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Show paired ends in contig overview |
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Create alignments with Clustal Omega |
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Move multiple gaps with drag&drop in contig view |
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Remove consensus gaps |
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Support for 64-bit Windows |
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Stacked and packed contig overview |
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Additional difference table filters |
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Contig overview printing |
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Speed improvements for large projects |
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Memory improvements for large projects |
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Show colored discrepancies in sample arrows |
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Display coverage with colored differences |
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Zooming for sample arrows in contig view |
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Import a subset of sequences |
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Build tree for selected bases only |
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Split contig by tree |
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Highlight sequences with labels |
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Read & write fastq files |
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Read sam files |
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Add tags to all samples at the same time |
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Support for larger projects |
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Faster assemblies & alignments |
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Make sequences upper / lower case |
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Replace gaps ('-') in consensus sequences |
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Neighbor-Joining trees |
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Percentage consensus |
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Contig view zooming for bases |
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Automatic ref. seq. shortening after alignment |
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Mask bases with low coverage |
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Set base numbers |
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Customize toolbars through popup |
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Automatic name scheme definition |
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Speed improvements for many contigs |
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Rebuild consensus |
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Support for bi-directional scrolling |
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Amino acid translation for all samples |
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Protein translation based background colors |
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Difference tables |
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Import directly from GenBank |
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Script menu |
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New script commands |
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Import 454 data (SFF files) |
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Create new text sequences |
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Support larger projects |
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Faster assemblies |
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Automatic memory use on Windows |
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Improved pen tablet support |
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Restriction maps |
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Align to reference in groups (by name) |
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Create sequence alignments with muscle |
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New consensus options |
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Automatically edit to match consensus sequence |
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Call secondary peaks |
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Change ambiguities to bases |
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Convert low quality bases to N |
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Print preview for all views |
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Split indels in pseudo-allels |
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Trace sharpening |
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Support scripting |
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Export unphased haplotypes |
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Improved mutation analysis |
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Large gap (cDNA to genomic) alignments |
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End-to-end assemblies & alignments |
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Improved detection of heterozygous indels |
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License Server support |
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Support NBRF/PIR format |
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Drag & drop folders on project view |
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Roundtrip editing |
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Contigs of contigs (align contigs) |
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Create alignments with ClustalW |
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Assemble in groups (by name) |
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One-step processing |
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Start BLAST searches |
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Mask bases matching the consensus sequence |
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Export protein translations |
For more details about those features, please look at the new feature descriptions of version 9, 8, 7, 6, 5, 4, 3.5, 3.0, 2.0, 1.6 and 1.5.