joint-indels(1)

NAME
joint-indels - Usage: joint-indels [OPTIONS]

SYNOPSIS
joint-indels alignments file trees file [OPTIONS]

DESCRIPTION
Usage: joint-indels [OPTIONS]

ALLOWED OPTIONS:

-h, –help
    produces help message

–subsample arg (=10)
    factor by which to sub-sample trees

–partition arg
    find indels along internal branch that bi-partitions given taxa (taxa1:taxa2:...)

–alphabet arg
    set to `Codons' to prefer codon alphabets

-V, –verbose
    [=arg(=1)] Show more log messages on stderr.

–extract-sequences arg
    Extract sequences corresponding to 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.