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% alignment-max(1)
% Benjamin Redelings
% Feb 2018
# 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>.
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