Prot2codon finds finds the codon-level (nucleotide) alignment implied by a given alignment at the amino acid level. Input protein alignment must be in multi-FASTA or Stockholm format and input nucleotide sequences must be in FASTA format.
Parent program: fsa
FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. FSA can be used for all alignment problems, including: detailed analysis of a single family of proteins or RNAs, large-scale alignment of thousands of sequences and genome alignment of megabases of orthologous sequences.