Provided by: bali-phy_3.6.1+dfsg-1_amd64
NAME
summarize-ancestors - Construct alignments with internal sequences for labeled nodes in query tree.
SYNOPSIS
summarize-ancestors alignment -A fastas1 -T trees1 [OPTIONS]
DESCRIPTION
Construct alignments with internal sequences for labeled nodes in query tree.
GENERAL OPTIONS:
-h, --help produces help message -V, --verbose [=arg(=1)] Show more log messages on stderr.
INPUT OPTIONS:
-A arg, --alignments arg File of alignment samples -T arg, --trees arg File of corresponding tree samples -x arg (=10), --subsample arg (=10) factor by which to sub-sample trees
ANCESTOR QUERY OPTIONS:
-n arg, --nodes arg Newick tree with labelled ancestors -g arg, --groups arg File with named groups --nodes-min arg (=0.34) Minimum fraction to include a node. --groups-min arg (=0.34) Minimum fraction to include a group.
EXAMPLES:
Add ancestral sequences to summary alignment: % summarize-ancestors summary.fasta -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree
REPORTING BUGS:
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <bali-phy-users@googlegroups.com>.
AUTHORS
Benjamin Redelings. Feb 2018 summarize-ancestors(1)