Slice_mercator_alignment extracts the corresponding subalignment from a Mercator multiple alignment (FSA–Mercator whole-genome alignment). This tool assumes that coordinates are 1-based and fully-closed, therefore representing the interval [start, end]. If requested, unmappable sequence will be truncated to the mappable portion; note that the truncation will favor the beginning of the requested sequence. If the requested sequence is on the - strand, then the corresponding subalignment will be reverse-complemented.
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.