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.TH "alignment-gild" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-gild\f[R] - Annotate each residue in the alignment
according to the probability that it should align to the hypothetical
root character in its column.
.SH SYNOPSIS
.PP
\f[B]alignment-gild\f[R] alignment-file tree-file ...
[OPTIONS] < alignments-file
.SH DESCRIPTION
.PP
Annotate each residue in the alignment according to the probability that
it should align to the hypothetical root character in its column.
.SH ALLOWED OPTIONS:
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
produce help message
.TP
\f[B]--align\f[R] \f[I]arg\f[R]
file with sequences and initial alignment
.TP
\f[B]--tree\f[R] \f[I]arg\f[R]
file with initial tree
.TP
\f[B]--find-root\f[R]
estimate the root position from branch lengths
.TP
\f[B]--alphabet\f[R] \f[I]arg\f[R]
set to \[aq]Codons\[aq] to prefer codon alphabets
.TP
\f[B]--skip\f[R] \f[I]arg\f[R] (=0)
number of alignment samples to skip
.TP
\f[B]--max-alignments\f[R] \f[I]arg\f[R] (=1000)
maximum number of alignments to analyze
.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.