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.TH "alignment-max" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-max\f[R] - Construct a posterior decoding alignment to
summarize an alignment sample.
.SH SYNOPSIS
.PP
\f[B]alignment-max\f[R] [OPTIONS] < alignments-file
.SH DESCRIPTION
.PP
Construct a posterior decoding alignment to summarize an alignment
sample.
.SH ALLOWED OPTIONS:
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
Produce help message
.TP
\f[B]--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]--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]--max-alignments\f[R] \f[I]arg\f[R] (=1000)
Maximum number of alignments to analyze
.TP
\f[B]--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]--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]--out-probabilities\f[R] \f[I]arg\f[R]
Output file for column probabilities, if specified
.TP
\f[B]-V\f[R], \f[B]--verbose\f[R]
Output more log messages on stderr.
.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.