Additional+Mesquite+Packages

=Additional Mesquite Packages=

Mesquite comes with many "packages" already installed. A package is a collection of features that are related in terms of their functions. For example, the Charts package that comes with Mesquite has numerous features for presenting results in chart form. Some of the packages distributed with the standard Mesquite are actually separate programming efforts, with a distinct development team. For example, Align is a package that was developed in conjunction with Travis Wheeler, and provides basic alignment tools within Mesquite.

However, there are additional packages that do not come with a basic Mesquite installation, and that must be installed separately. The ones we are aware of are listed below.

Zephyr
Zephyr enables Mesquite to interact with phylogenetic inference programs such as RAxML and GARLI. For example, Zephyr will send a matrix to be analyzed by RAxML, start up RAxML to begin a likelihood search, monitor the run as it progresses (showing you intermediate trees as RAxML searches), and then harvest and display the trees to you automatically once the search is completed.

PDAP: PDTREE
Peter Midford, Ted Garland and Wayne Maddison have released a Mesquite version of [|PDAP:PDTree], which analyzes continuous-valued data in a phylogenetic context using Independent Contrasts.

TreeSetViz
A team of computer scientists and biologists from the University of Texas, Lehman College and University of California Davis have developed [|Tree Set Viz], a set of Mesquite modules for calculating consensus trees and for visualizing sets of trees according to their similarities.

[[image:Chromaseqsplash.gif]]
For deriving and editing DNA sequences from chromatograms, [|Chromaseq] provides integration of chromatogram viewing and base calling with Mesquite's matrix editor, alignment and other functions.

** Opal and Opalescent **
Travis Wheeler and John Kececioglu have released a version of Opal, a multiple sequence alignment program, that functions from within Mesquite using the Opalescent package by Travis Wheeler and David Maddison. Details are available on the [|Opalescent] page.

** Mesquite.R **


Wayne Maddison and Hilmar Lapp have made [|Mesquite.R], which enables access to some functions in the ape and diversitree packages in the statistical language R. A companion [|RMesquite] enables access to Mesquite from R.

[[image:Cartographersplash.gif]]
David Maddison & Wayne Maddison have developed [|Cartographer], a package of modules for plotting species distributions ("dot maps") and for plotting phylogenies on maps.

[[image:hyphaSplash.gif]]
Jeff Oliver developed [|Hypha], a package of modules designed for displaying tree support values from multiple sources, in the form of colored grids on nodes.

NINJA
Travis Wheeler has released [|NINJA], a fast Neighbor Joining method for phylogenetic tree inference. You can install NINJA in Mesquite using instructions [|here].

** AUGIST **
Jeff Oliver has developed [|AUGIST], which infers species trees considering the uncertainty in gene genealogies.

** CoMET **
Lee, Blay, Mooers, Singh, & Oakley have developed [|CoMET], a package for comparing models of continuous character evolution on phylogenies.

** StratigraphicTools ** and ** StratAdd **
Michel Laurin has coordinated the development of two packages of modules with tools for integrating [|stratigraphy with phylogeny].

** SILK **
Wayne Maddison & Martín Ramírez have produced [|SILK (Simple Image LinKing)], a package to integrate images into morphological data coding, in collaboration with the spider ATOL project.

** Tuatara **
Wayne Maddison & Arne Mooers have released [|Tuatara], a package of modules for analyzing conservation priorities in a phylogenetic context.

** LASRDisc **
Vanessa Jackson released [|LASRDisc], which reconstructs ancestral states of categorical characters by likelihood, providing more options than those in the built-in stochchar package of Mesquite. This package is no longer under development and does not work with the current version of Mesquite.

Installing Additional Packages
The method of installing additional packages varies depending upon the package. There two common mechanisms for installation:


 * 1) The documentation for the package may contain an installation URL. For example, on the home page of [|TreeSetViz], there is the following installation URL listed: http://mesquiteproject.org/packages/tsv/install.xml If you enter this URL into the File>Check Now for Notices/Installs dialog box, Mesquite will download the information at that URL and proceed to install TreeSetViz.
 * 2) If there is no installation URL, then you will probably need to install the package manually. The simplest way to do that is to place the folder containing the package into the "mesquite" folder that is contained within your Mesquite_Folder. For example, if you want to install [|Cartographer], then you will need to download the relevant file on the [|download page] . This file, when unarchived, contains two directories, one of which is called "Put in Mesquite Directory". In that folder is one folder called "cartographer". In general, you will need to find the folder (not a zip file, or dmg file, but the folder) that has the name of the package. That folder ("cartographer" in this case) should then be moved into the "mesquite" folder within "Mesquite_Folder". For more details about where module packages should reside, see the section of module locations.