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, wsum2, 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>.

AUTHORS

Benjamin Redelings.