The Garli Wiki
Creators: name: Zwickl, Derrick
Publisher: name: Zenodo
Year: 2015
Subjects: phylogenetic inference
phylogenetics
phylogeny inference
maximum likelihood

description: <em>This is a snapshot of the support wiki for GARLI, a phylogenetic tree reconstruction tool. The wiki was live at https://www.nescent.org/wg_garli/Main_Page</em>

<strong>What is GARLI?</strong>

GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. Version 2.0 adds support for partitioned models and morphology-like datatypes. It is usable on all operating systems, and is written and maintained by Derrick Zwickl (zwickl{at}ku{dot}edu or garli.support{at}gmail{dot}com).

<strong>Obtaining GARLI</strong>

Current Version


	<strong>GARLI 2.0 has been released (April 2011)! You can download it at the GARLI page on Google Code: http://garli.googlecode.com</strong>


GARLI 2.0 is first "official" release including partitioned models. It is a merging of official release 1.0 and beta version GARLI-PART 0.97. Version 2.0 should replace earlier versions, and should be backwards compatible with all configuration files and datasets that were used with either Version 1.0 or GARLI-PART 0.97. See this page for a more complete listing of changes: Version changes.

Older Versions


	The previous version 1.0 (Dec 09) can still be found on Google Code:  http://garli.googlecode.com
	The most recent version with a GUI (0.951) is still available here: Download page


<strong>Documentation and support for GARLI</strong>

There are a number of options:


	This wiki contains an online Manual which contains a full description of the <strong>GARLI Configuration Settings</strong>, an <strong>FAQ</strong> and a <strong>Brief_tutorial</strong>. Lots of other information appears on the wiki as well.
	Alternatively, you can download an older version of the manual in pdf format from here. (Scroll down to "Available Packages" and choose "Manual for Version 0.96"). Note that the information on the wiki is MUCH more up to date than that in the pdf manual, and no information on partitioned models appears in the manual at all.
	Questions may be posted to a new GARLI user forum has been created through the garli_users google group.
	You may also email questions and problems to garli{dot}support{at}gmail{dot}com


Recent additions to the wiki


	Details on setting up partitioned models: <strong>Using partitioned models</strong>
	New FAQ item: <strong>Help with GARLI compilation from source code</strong>
	Details on specifying an amino acid model not specifically implemented by GARLI (for example, the LG model). Version 1.0 and later: <strong>Specifying a custom amino acid rate matrix</strong>
	Brief descriptions of changes in versions 1.0 and 2.0: <strong>Version changes</strong>
	Advanced topics page that gives a more in depth discussion of GARLI usage and interpretation of results: <strong>Advanced_topics</strong>
	Documentation and usage information for the parallel MPI version: <strong>MPI_version</strong>
	New FAQ item <strong>"MODELTEST told me to use model X. How do I set that up in GARLI?"</strong>.


<strong>Citing GARLI</strong>

If you use GARLI please cite 


Zwickl, D. J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.
description: Instructions on how to import the dump into a MediaWiki instance can be found at MediaWiki: https://www.mediawiki.org/wiki/Manual:Importing_XML_dumps. Every dump consists of two files, an .xml.gz and a .tar.gz. The .xml.gz is
processed by importDump.php, the .tar.gz is processed by importImages.php,
as per the above documentation.