extract-ancestors

NAME

extract-ancestors - Extract and name ancestral sequences according to node- and branch- queries.

SYNOPSIS

extract-ancestors [OPTIONS]

DESCRIPTION

Extract and name ancestral sequences according to node- and branch- queries.

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 named ancestral sequences to alignments where they are present:

% extract-ancestors -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.