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

-m arg (=500), –max arg (=500)

Thin (alignment,tree) pairs down to this number of samples.

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.