NAME¶
garli - phylogenetic analysis of molecular sequence data using
maximum-likelihood (MPI version)
SYNOPSIS¶
mpirun [MPI OPTIONS] garli-mpi -[# of times to execute
config file] [config filename]
DESCRIPTION¶
GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
inferring phylogenetic trees. Using an approach similar to a classical genetic
algorithm, it rapidly searches the space of evolutionary trees and model
parameters to find the solution maximizing the likelihood score. It implements
nucleotide, amino acid and codon-based models of sequence evolution, and runs
on all platforms. The latest version adds support for partitioned models and
morphology-like datatypes. This is the MPI version of Garli.
OPTIONS¶
- -i, --interactive
- interactive mode (allow and/or expect user feedback)
- -b, --batch
- batch mode (do not expect user input) (batch is the default for the
version you are running)
- -v, --version
- print version information and exit
- -h, --help
- print this help and exit
- -t
- run internal tests (requires dataset and config file)
- -V
- validate: load config file and data, validate config file, data, starting
trees and constraint files, print required memory and selected model, then
exit
NOTE: If no config filename is passed on the command line the
program will look in the current directory for a file named
"garli.conf"
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.
