Isect_mercator_alignment_gff extracts subalignments from a Mercator multiple alignment for the features in the GFF file. While this program is reasonably fast if the GFF is properly ordered by chromosome and the start and end coordinates of features, it will be *very slow* if the GFF is not sorted. Assumes that the 'seqid' or 'name' field (the first field) of the GFF entries holds the chromosome name. Note that the GFF specification defines coordinates to be 1-based and fully-closed, therefore representing the interval [start, end]. Conformance to this specification is assumed internally. If requested, unmappable sequence will be truncated to the mappable portion; note that the truncation will favor the beginning of the requested sequence.
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.