PAL2NAL -- robust conversion of protein sequence alignments into the corresponding codon alignments
What you can do:
Convert a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.
Highlights:
- PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences.
- The server takes a protein sequence alignment and the corresponding DNA sequences as input. In contrast to other existing applications, this server is able to construct codon alignments even if the input DNA sequence has mismatches with the input protein sequence, or contains untranslated regions and polyA tails.
- If the input is a pair of sequences, PAL2NAL automatically calculates KS and KA by the codeml program in PAML.
- The server can also deal with frame shifts and inframe stop codons in the input models, and is thus suitable for the analysis of pseudogenes.
Keywords:
- multiple protein sequence alignment
- condon conversion tool
- condon alignment analysis tool
- condon usage analysis tool
- nucleotide substitution rate
- gene selection
- phylogenetic analysis
Literature & Tutorials:
This record last updated: 04-18-2014