bbFilter - this is a part of mauveAligner package

bbFilter<backbonefile><independentdist><outputfile><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

bbFilter 1.2.0+4713                                April 2015                                        BBFILTER(1)

       bbFilter - this is a part of mauveAligner package