Recent Changes

Friday, May 4

  1. page space.menu edited Mesquite Home Page Overview of Mesquite What Mesquite Does List of Features Recent Changes …

    Mesquite Home Page
    Overview of Mesquite
    What Mesquite Does
    List of Features
    Recent Changes
    Development Team
    Contact Us
    Getting Started
    Download and Installation
    Additional Packages
    Beginning Mesquite
    Example Files
    Basics
    Files
    Menus
    Windows
    Charts
    Selection
    Modules
    Simplifying Mesquite
    Objects
    Characters
    Taxa
    Trees
    Analyses
    Character Evolution
    Diversification
    Molecular Data
    Gene Trees
    Simulations & Randomizations
    Continuous Characters
    Studies of Tree Topology
    Workflows
    Managing Molecular Data
    Managing Continuous Data
    Interactions with other programs
    Getting Help
    Learning Mesquite
    Bugs & Troubleshooting
    Getting Help
    Your Suggestions
    Glossary
    FAQ
    Technical Details
    How Mesquite Works
    Scripts & Macros
    Source Code
    Developer's Documentation
    History
    History of Mesquite
    Why Mesquite?
    New Features & Bug List
    Release Dates
    Publishing Results
    Documenting your work
    Citing Mesquite
    Publishing results
    Acknowledgements

    (view changes)
    3:04 pm
  2. page home edited If you're looking for Mesquite Software, Inc. or its CSIM toolkit for building simulation models, g…
    If you're looking for Mesquite Software, Inc. or its CSIM toolkit for building simulation models, go here
    Mesquite: A modular system for evolutionary analysis
    Current release version: 3.4 [download]
    If you have a previous version, please update because of bug fixes and
    The new features.
    Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.
    {analysesMedley.jpg}
    Mesquite also has many features for managing and processing data, including processing of chromatograms, sequence alignment, editing of morphometric data, and others.
    {HomePageData.jpg}
    More examples of Mesquite's features can be found in What Mesquite Does. There is also an outline of Mesquite's features. Additional packages can be installed to extend Mesquite's capabilities to interacting with RAxML and other tree-inference programs, processing chromatograms and making base calls, tree set visualization, and so on.
    This wiki introduces you to the Mesquite system for analysis in evolutionary biology. Its organization follows the manual of Mesquite 2.75, but we are planning to restructure it to serve as a better introduction to Mesquite's use. Some aspects of this documentation may be out of date, for example referring to menus that have moved or been renamed. If you find an obsolete reference, please contact us at info {at} mesquiteproject.org.
    Getting started
    To begin using Mesquite on the Mac OS, Unix/Linux or Windows, see the installation instructions. We encourage you to explore the example files in the "examples" directory of the Mesquite_Folder.
    Once you have installed Mesquite, we recommend that you read the Learning
    Mesquite web page to learn how best to become familiar Mesquite. And, although reading the documentation on this wiki will help, not all features are described here. Because many analyses are possible and those available depend on what modules are installed and loaded, a comprehensive manual cannot easily be written. For this reason, many analyses available in Mesquite are not included in any written manual. It is thus important to learn how to discover Mesquite's capabilities from the program itself, and documented on the Learning Mesquite page. You are encouraged to explore, and invent new analyses.
    Should you wish to install additional features that are beyond the core Mesquite installation, please see the page on Installing Additional Packages.
    Mesquite is complex, but it is approachable
    Because its modularity, and the zeal of the development team, Mesquite has many, many options. This give it a lot of power, as it enables complex, custom-built analyses, but it also means that it can be rather complex if you only want to do something simple. The interface is also a bit unusual, and needs to be learned. However, by reading the documentation, watching the Youtube videos, and following through the example files, you will find that it can be quite approachable.
    If you encounter problems
    We encourage you to report bugs or misbehaviour of Mesquite. You may find a problem that seems so obvious to you that you expect we must have seen it. Please report it anyway, because perhaps it occurs only in particular circumstances that we didn't test, or it occurs with a combination of options that we haven't tested recently. The Bugs and Troubleshooting page has more details on reporting bugs.
    Conventions of this wiki
    For compactness, we will use a special convention to refer to menu items. For example,File>Save File refers to the Save File menu item of the File menu. (Tree Window)Display>Tree Form>Diagonal Tree refers to the Diagonal Tree menu item of the Tree Form submenu of the Display menu that is associated with the Tree Window. By referring to a menu as "associated with" a window, we mean that that menu is present in the menu bar
    at the top of the screen when the window is frontmost (on the MacOS), or that the menu is embedded within the window (on the Windows OS and most other operating systems).http://www.mesquiteproject.org
    (view changes)
    3:03 pm

Saturday, April 7

  1. page History of New Features edited ... Bug Fixes and Workarounds Scrolling in various windows using the scroll wheel is sometimes ve…
    ...
    Bug Fixes and Workarounds
    Scrolling in various windows using the scroll wheel is sometimes very chaotic. This is a bug not in Mesquite but one introduced into Java 1.8 update 161. A workaround was introduced into Mesquite Build 879.
    Scrolling with the scroll wheel sometimes caused Mesquite to freeze. Fixed in build 881.
    Can now read CharSet token embedded within a CharPartition command in the NEXUS file. Build 884.
    Verstion 3.40
    (view changes)
    11:17 am
  2. page History of New Features edited ... Bug Fixes and Workarounds Scrolling in various windows using the scroll wheel is sometimes ve…
    ...
    Bug Fixes and Workarounds
    Scrolling in various windows using the scroll wheel is sometimes very chaotic. This is a bug not in Mesquite but one introduced into Java 1.8 update 161. A workaround was introduced into Mesquite Build 879.
    Can now read CharSet token embedded within a CharPartition command in the NEXUS file. Build 884.
    Verstion 3.40
    New Features
    (view changes)
    11:15 am

Saturday, February 10

  1. page History of New Features edited ... none yet Bug Fixes and Workarounds ... chaotic. This appears to be is a bug ... update…
    ...
    none yet
    Bug Fixes and Workarounds
    ...
    chaotic. This appears to beis a bug
    ...
    update 161. We will be lookingA workaround was introduced into workarounds.Mesquite Build 879.
    Verstion 3.40
    New Features
    (view changes)
    9:48 pm

Sunday, February 4

  1. page History of New Features edited ... none yet Bug Fixes and Workarounds none yet Scrolling in various windows using the scroll …
    ...
    none yet
    Bug Fixes and Workarounds
    none yetScrolling in various windows using the scroll wheel is sometimes very chaotic. This appears to be a bug not in Mesquite but one introduced into Java 1.8 update 161. We will be looking into workarounds.
    Verstion 3.40
    New Features
    (view changes)
    10:55 am

Saturday, January 27

  1. page How to Cite Mesquite edited ... Citing the software system in general The citation for this version of the Mesquite sofware i…
    ...
    Citing the software system in general
    The citation for this version of the Mesquite sofware is:
    ...
    D.R. Maddison. 2017.2018. Mesquite: a
    ...
    analysis. Version 3.313.40 http://mesquiteproject.org
    (The version number listed above might not be up to date. Check the Mesquite Startup window or the Project and Files window when Mesquite is running to find the version you have.)
    If you are using an additional Mesquite package (e.g., PDAP, Zephyr, TreeSetViz,Hypha, Chromaseq) you may need to cite that as well; check the documentation of that package for citation information.
    Citing the documentation
    The citation for this documentation is:
    ...
    Project Team. 2017.2018. Documentation for
    evolutionary analysis. https://mesquiteproject.wikispaces.com
    You should probably include the access date and the specific page to which you are referring in the citation.
    Note that there are a few pages in this documentation that have separate authorship and citation requirements; please check to see if the page you are citing is so marked.
    analysesCiting Mesquite for analyses done
    ...
    and Maddison, 2016);2018); its null
    Doe, J. 2012. SNIDIND: a Mesquite module for calculating the Snidely Index,
    version 3.5.
    ...
    D.R. Maddison. 2017.2018. Mesquite: a
    ...
    analysis. Version 3.31 http://mesquiteproject.org.3.40
    http://mesquiteproject.org.

    Za, T. 2014. SimSpeciation: a package of modules to simulate evolutionary
    trees. Version 3.14159.
    (view changes)
    12:29 pm
  2. page Release Dates edited ... First Build Date 3.40 877 27 January 2018 3.31 858
    ...
    First Build
    Date
    3.40
    877
    27 January 2018

    3.31
    858
    (view changes)
    12:22 pm
  3. page History of New Features edited ... There is also a list of release dates. Features in the next release version of Mesquite; the …
    ...
    There is also a list of release dates.
    Features in the next release version of Mesquite; the latest source code in the development branch of the MesquiteProject/MesquiteCore repository on GitHub contains these changes
    New Features
    none yet
    Bug Fixes and Workarounds
    none yet
    Verstion 3.40

    New Features
    A new tool has been added to the data matrix window for non-molecular categorical data, the Popup State Entry tool. When touched on a cell, a popup menu will appear that lists the states for that character, allowing easy data entry if the states are named.
    (view changes)
    12:15 pm
  4. page home edited If you're looking for Mesquite Software, Inc. or its CSIM toolkit for building simulation models, g…
    If you're looking for Mesquite Software, Inc. or its CSIM toolkit for building simulation models, go here
    Mesquite: A modular system for evolutionary analysis
    ...
    release version: 3.313.4 [download]
    If you have a previous version, please update because of bug fixes and new features.
    Warning: Mesquite does not work under Java 9 because of major new restrictions imposed by Oracle on the way Java applications can be structured. We are working on a fix for this, and should release it in January. In the meantime, do not install Java 9 if you wish to use Mesquite.
    Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.
    {analysesMedley.jpg}
    (view changes)
    12:13 pm

More