CodonAlign 2.0
Alignment of DNA sequences requires the introduction of gaps that represent
historical insertions and deletions. Direct alignment of protein coding
sequences results in the introduction of gaps that, when the gapped sequences
are translated, result in frame-shifted proteins that bear no resemblence
to the original proteins or to each other. Historically, the insertions and
deletions represented by those gaps would have caused non-functional proteins
that would have been removed by purifying selection. A more realistic alignment
can be obtained by first aligning the proteins themselves, then introducing
into the corresponding DNA coding sequences triplet-gaps at the positions
corresponding to each gap in the protein sequence. Translation of those
sequences recovers the original protein sequences. CodonAlign 2.0 produces
an alignment of DNA coding sequences based on an input protein
alignment and a file of corresponding DNA coding sequences.
Three packages are available: Macintosh, Windows, and UNIX. The Macintosh
and Windows packages include the compiled CodonAlign 2.0 program ready
to run on that platform. The UNIX package includes the source code and
a MAKE file that can be compiled on the individual UNIX platform machine.
All packages include documentation and example input files.
Download
the Macintosh Package as a Stuffit archive. CodonAlign 2.0 runs
undr both Classic and OSX.
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