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