extract-ancestors1

Usage

Overview

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⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .