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.TH "alignment\-consensus" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-consensus\f[] \- Construct a consensus alignment to
summarize an alignment sample.
.SH SYNOPSIS
.PP
\f[B]alignment\-consensus\f[] [OPTIONS] < alignments\-file
.SH DESCRIPTION
.PP
Construct a consensus 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]\-\-seed\f[] \f[I]arg\f[]
random seed
.RS
.RE
.TP
.B \f[B]\-\-skip\f[] \f[I]arg\f[] (=0)
number of tree samples to skip
.RS
.RE
.TP
.B \f[B]\-\-max\-alignments\f[] \f[I]arg\f[] (=1000)
maximum number of alignments to analyze
.RS
.RE
.TP
.B \f[B]\-\-strict\f[] \f[I]arg\f[]
ignore events below this probability
.RS
.RE
.TP
.B \f[B]\-\-cutoff\f[] \f[I]arg\f[]
ignore events below this probability
.RS
.RE
.TP
.B \f[B]\-\-uncertainty\f[] \f[I]arg\f[]
file\-name for AU uncertainty vs level
.RS
.RE
.TP
.B \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.