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| author | Petar Petrov <slackalaxy@gmail.com> | 2017-10-07 21:14:04 +0100 |
|---|---|---|
| committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2017-10-11 06:19:51 +0700 |
| commit | 7f80fb2d089a8239eb5fa550000b2af3dbe08596 (patch) | |
| tree | 721a2954fbe35a5df4dd34814006777d38ffa451 /academic/pal2nal/README | |
| parent | 267f7f66099b2f8d842d8531e77feb1d671b547e (diff) | |
| download | slackbuilds-7f80fb2d089a8239eb5fa550000b2af3dbe08596.tar.gz | |
academic/pal2nal: Added (Create a codon-based DNA alignment).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
Diffstat (limited to 'academic/pal2nal/README')
| -rw-r--r-- | academic/pal2nal/README | 17 |
1 files changed, 17 insertions, 0 deletions
diff --git a/academic/pal2nal/README b/academic/pal2nal/README new file mode 100644 index 0000000000..db752e12bc --- /dev/null +++ b/academic/pal2nal/README @@ -0,0 +1,17 @@ +PAL2NAL is a program that converts a multiple sequence alignment of +proteins and the corresponding DNA (or mRNA) sequences into a codon- +based DNA alignment. The program automatically assigns the corresponding +codon sequence even if the input DNA sequence has mismatches with the +input protein sequence, or contains UTRs,polyA tails. It can also deal +with frame shifts in the input alignment, which is suitable for the +analysis of pseudogenes. + +The resulting codon-based DNA alignment can further be subjected to the +calculation of synonymous (Ks) and non-synonymous (Ka) substitution +rates. + +If you use PAL2NAL, please cite the following paper: + +Mikita Suyama, David Torrents, and Peer Bork (2006) +PAL2NAL: robust conversion of protein sequence alignment into the +corresponding codon alignments. Nucleic Acids Res. 34:W609-W612. |