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extract-ancestors(1) extract-ancestors(1)

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:

produces help message
[=arg(=1)] Show more log messages on stderr.

INPUT OPTIONS:

File of alignment samples
File of corresponding tree samples
factor by which to sub-sample trees

ANCESTOR QUERY OPTIONS:

Newick tree with labelled ancestors
File with named groups
Minimum fraction to include a node.
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.

Feb 2018