garli1

Usage

Overview

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.

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"