NAME

alignment-max -- Construct a posterior decoding alignment to summarize an alignment sample.

SYNOPSIS

alignment-max [OPTIONS] < alignments-file

DESCRIPTION

Construct a posterior decoding alignment to summarize an alignment sample.

ALLOWED OPTIONS:

-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.

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.