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

--details

Output detailed indel information (Start/End positions, I/D type, lengths). See https://github.com/bredelings/BAli-Phy/blob/master/tests/tools/joint-indels/README.md for output format documentation.

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.