Slice_fasta_gff extracts a subsequence from an input FASTA file. Assumes 1-based, fully-closed coordinates, but unlike slice_fasta it requires user to provide a GFF file with coordinates. Coordinates from this GFF file will be used to make a slice (subset) of sequences. This tool is capable of producing a reverse-complemented sequence to the requested slice.
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.