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diff --git a/academic/pal2nal/README b/academic/pal2nal/README new file mode 100644 index 000000000000..db752e12bcb4 --- /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. |