bbFilter - this is a part of mauveAligner package
bbFilter <backbone file> <independent dist> <output
file> <beast|gp> [<seq1> <seq2>...<seqN>]
seq index starts at 0.
Example:
-
bbFilter my_alignment.backbone 50 my_feats.bin
gp
the above command extracts binary features from
"my_alignment.backbone" which are separated by a minimum of 50nt
sequence conserved among all taxa in the alignment. The output is written to
my_feats.bin in genoplast format
Example 2:
-
bbFilter aln.backbone 100 feats.xml beast 0 1 2 5
6
the above command extracts binary features from "aln.backbone" which
are separated by a minimum of 100nt sequence conserved among genomes 0,1,2,5,
and 6 from the alignment. The output is written to feats.xml in beast
format