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

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.

                                             Feb 2018                      summarize-ancestors(1)