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)

Tree stride used to match alignment records. Use 1 for already-paired files.

--skip n (=0), --until n

First and last original tree-record positions to retain, inclusive and zero-based. With original BAli-Phy logs these are iteration numbers. The default has no upper bound.

--thin k (=1)

Keep every kth eligible alignment/tree pair, starting with the first eligible pair in each chain.

-m arg (=500), --max arg (=500)

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

Alignment record j is paired with tree record j times the tree stride before selection. Both input files must therefore start at corresponding samples. For already-filtered files, the bounds refer to positions in those files, not to discarded original iteration labels. The maximum sample count is applied after selection and thinning.

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.