alignment-max - Construct a posterior decoding alignment to
summarize an alignment sample.
alignment-max [OPTIONS] < alignments-file
Construct a posterior decoding alignment to summarize an alignment
sample.
- -h,
--help
- Produce help message
- --alphabet
arg
- Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets,
Codons, or Codons+stop.
- -s arg (=0),
--skip arg (=0)
- Number of alignment samples to skip
- -m arg (=1000),
--max-alignments arg (=1000)
- Maximum number of alignments to analyze
- --analysis
arg (=wsum)
- sum, wsum, multiply
- -o arg (=-),
--out arg (=-)
- Output file (defaults to stdout)
- -p arg,
--out-probabilities arg
- Output file for column probabilities, if specified
- -v,
--verbose
- Output more log messages on stderr.
BAli-Phy online help:
<http://www.bali-phy.org/docs.php>.
Please send bug reports to
<bali-phy-users@googlegroups.com>.