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.TH "alignment\-gild" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-gild\f[] \- 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[] 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
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
produce help message
.RS
.RE
.TP
.B \f[B]\-\-align\f[] \f[I]arg\f[]
file with sequences and initial alignment
.RS
.RE
.TP
.B \f[B]\-\-tree\f[] \f[I]arg\f[]
file with initial tree
.RS
.RE
.TP
.B \f[B]\-\-find\-root\f[]
estimate the root position from branch lengths
.RS
.RE
.TP
.B \f[B]\-\-alphabet\f[] \f[I]arg\f[]
set to \[aq]Codons\[aq] to prefer codon alphabets
.RS
.RE
.TP
.B \f[B]\-\-skip\f[] \f[I]arg\f[] (=0)
number of alignment 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]\-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.