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