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GARLI(1) User Commands GARLI(1)


garli - phylogenetic analysis of molecular sequence data using maximum-likelihood


garli [OPTION] [config filename]


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.


-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
run internal tests (requires dataset and config file)
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"


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
June 2016 garli 2.1