.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH GARLI "1" "June 2016" "garli 2.1" "User Commands"
.SH NAME
garli \- phylogenetic analysis of molecular sequence data using maximum-likelihood
.SH SYNOPSIS
.B garli
[\fI\,OPTION\/\fR] [\fI\,config filename\/\fR]
.SH 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.
.SH OPTIONS
.TP
\fB\-i\fR, \fB\-\-interactive\fR
interactive mode (allow and/or expect user feedback)
.TP
\fB\-b\fR, \fB\-\-batch\fR
batch mode (do not expect user input)
(batch is the default for the version you are running)
.TP
\fB\-v\fR, \fB\-\-version\fR
print version information and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
print this help and exit
.TP
\fB\-t\fR
run internal tests (requires dataset and config file)
.TP
\fB\-V\fR
validate: load config file and data, validate config file, data, starting trees
and constraint files, print required memory and selected model, then exit
.P
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"
.PP
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.