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.TH "summarize-ancestors" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]summarize-ancestors\f[R] - Construct alignments with internal
sequences for labeled nodes in query tree.
.SH SYNOPSIS
.PP
\f[B]summarize-ancestors\f[R] \f[I]alignment\f[R] -A \f[I]fastas1\f[R]
-T \f[I]trees1\f[R] [OPTIONS]
.SH DESCRIPTION
.PP
Construct alignments with internal sequences for labeled nodes in query
tree.
.SH GENERAL OPTIONS:
.TP
\f[B]-h\f[R], \f[B]\[en]help\f[R]
produces help message
.TP
\f[B]-V\f[R], \f[B]\[en]verbose\f[R]
[=arg(=1)] Show more log messages on stderr.
.SH INPUT OPTIONS:
.TP
\f[B]-A\f[R] \f[I]arg\f[R], \f[B]\[en]alignments\f[R] \f[I]arg\f[R]
File of alignment samples
.TP
\f[B]-T\f[R] \f[I]arg\f[R], \f[B]\[en]trees\f[R] \f[I]arg\f[R]
File of corresponding tree samples
.TP
\f[B]-x\f[R] \f[I]arg\f[R] (=10), \f[B]\[en]subsample\f[R] \f[I]arg\f[R] (=10)
factor by which to sub-sample trees
.SH ANCESTOR QUERY OPTIONS:
.TP
\f[B]-n\f[R] \f[I]arg\f[R], \f[B]\[en]nodes\f[R] \f[I]arg\f[R]
Newick tree with labelled ancestors
.TP
\f[B]-g\f[R] \f[I]arg\f[R], \f[B]\[en]groups\f[R] \f[I]arg\f[R]
File with named groups
.TP
\f[B]\[en]nodes-min\f[R] \f[I]arg\f[R] (=0.34)
Minimum fraction to include a node.
.TP
\f[B]\[en]groups-min\f[R] \f[I]arg\f[R] (=0.34)
Minimum fraction to include a group.
.SH EXAMPLES:
.PP
Add ancestral sequences to summary alignment:
.IP
.nf
\f[C]
% summarize-ancestors summary.fasta -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree
\f[R]
.fi
.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.