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 (=multiply)

sum, wsum, wsum2, multiply

--column-pr arg (=homology)

homology, alignment

-S arg (=1), --sort arg (=1)

Sort partially ordered columns to group similar gaps

-o arg (=-), --out arg (=-)

Output file (defaults to stdout)

-p arg, --out-probabilities arg

Output file for column probabilities, if specified

--debug-graph arg

Filename for debug graph

-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.