Bio-BPWrapper
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=item --gap-char '.'
Change '.' (e.g., from BCFtools, which causes problem for --uniq-seq) to default gap character '-'
=item --gap-states
Prints one alignment gap per line, including its start, end, whether in-frame, whether on-edge, how many copies, and alignment length. (Can't remember what context this was developed at first; ignore)
=item --gap-states2
Prints one alignment gap per column, including its start-end as column heading and presence/absence (1/0) in each sequence.
=item --input, -i 'format'
Now it tries to guess the format. BLAST outputs still need to be specified
[Deprecated except for blast output] Specify input file format. Common ones include 'clustalw' (default), 'fasta' and 'phylip'. See L<Bio::AlignIO> for supported formats.
In addition, it reads NCBI-blast outputs as well. e.g., bioaln -i'blast' blast.out.
=item --length, -l
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