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.TH "alignment\-max" "1" "Feb 2018" "" ""
.SH NAME
\f[B]alignment\-max\f[R] \- Construct a posterior decoding alignment to
summarize an alignment sample.
.SH SYNOPSIS
\f[B]alignment\-max\f[R] [OPTIONS] < alignments\-file
.SH DESCRIPTION
Construct a posterior decoding alignment to summarize an alignment
sample.
.SH ALLOWED OPTIONS:
.TP
\f[B]\-h\f[R], \f[B]\[en]help\f[R]
Produce help message
.TP
\f[B]\[en]alphabet\f[R] \f[I]arg\f[R]
Specify the alphabet: DNA, RNA, Amino\-Acids, Amino\-Acids+stop,
Triplets, Codons, or Codons+stop.
.TP
\f[B]\-s\f[R] \f[I]arg\f[R] (=0), \f[B]\[en]skip\f[R] \f[I]arg\f[R] (=0)
Number of alignment samples to skip
.TP
\f[B]\-m\f[R] \f[I]arg\f[R] (=1000), \f[B]\[en]max\-alignments\f[R] \f[I]arg\f[R] (=1000)
Maximum number of alignments to analyze
.TP
\f[B]\[en]analysis\f[R] \f[I]arg\f[R] (=wsum)
sum, wsum, wsum2, multiply
.TP
\f[B]\-o\f[R] \f[I]arg\f[R] (=\-), \f[B]\[en]out\f[R] \f[I]arg\f[R] (=\-)
Output file (defaults to stdout)
.TP
\f[B]\-p\f[R] \f[I]arg\f[R], \f[B]\[en]out\-probabilities\f[R] \f[I]arg\f[R]
Output file for column probabilities, if specified
.TP
\f[B]\-V\f[R], \f[B]\[en]verbose\f[R]
Output more log messages on stderr.
.SH REPORTING BUGS:
BAli\-Phy online help: \c
.UR http://www.bali-phy.org/docs.php
.UE \c
\&.
.PP
Please send bug reports to \c
.MT bali-phy-users@googlegroups.com
.ME \c
\&.
.SH AUTHORS
Benjamin Redelings.