Map_coords maps coordinates from one genome to another using a Mercator multiple alignment. This tool assumes that coordinates are 1-based and fully-closed, therefore representing the interval [start, end]. It uses the base-level homology mapping implied by a FSA–Mercator whole-genome alignment.
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.