Recent Changes

Sunday, January 7

  1. page History of New Features edited ... A new tool has been added to the data matrix window for non-molecular categorical data, the Po…
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    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.
    Bug Fixes and Workarounds
    Mesquite can now run under Java 9. Build 875.
    The classpaths.xml file has a new format; it is now a simple text file (classpaths.txt) with the paths listed one per line.

    Alignment using ClustalW was broken. Fixed in build 860.
    Matrices formed using the Concatenate Selected Matrices feature sometimes omitted state names that were present in the original matrices. Fixed in build 861.
    (view changes)
    1:10 pm

Monday, January 1

  1. page Modules edited ... in Mesquite_Folder/additionalMesquiteModules/mesquite: this is an optional location for module…
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    in Mesquite_Folder/additionalMesquiteModules/mesquite: this is an optional location for modules. If you are installing 3rd party modules, you might want to install them here, so that you can easily find them again and reinstall them when you upgrade to a newer version of Mesquite. If installed here, our example module would be at: Mesquite_Folder/additionalMesquiteModules/mesquite/mypackage/MyModule/MyModule.class
    in Mesquite_Support_Files/classes/mesquite: this is an optional location for modules. It can be useful for users who don't have permission to modify the main Mesquite_Folder but may want to install new modules. If installed here, our example module would be at: Mesquite_Support_Files/classes/mesquite/mypackage/MyModule/MyModule.class
    ...
    specified in a text file. In Mesquite 3.4 and later, this should be a simple text file called classpaths.txt that is in Mesquite_Folder (i.e., Mesquite_Folder/classpaths.txt). In Mesquite 3.31 and earlier it is in an XML file Mesquite_Folder/classpaths.xml. ThisThe simple text file for 3.4 and later should have
    ...
    as follows:
    ../MyExtraModules
    ../MoreExtraModules
    To disable a path, put a number/pound symbol (#) in front of it.
    The format for the XML file for Mesquite 3.31 and earlier is:

    <?xml version="1.0"?>
    <mesquite>
    <classpath>../MyExtraModules</classpath>
    </mesquite> This
    This
    tells Mesquite
    Furthermore, the active configuration must specify that the module's package be loaded. By default, all installed packages are loaded.
    Thus, if you open up the Mesquite_Folder, you might see the following
    (view changes)
    1:47 pm

Sunday, December 31

  1. page Source Code edited ... Mesquite packages that are distributed separately from Mesquite (e.g., Cartographer) are organ…
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    Mesquite packages that are distributed separately from Mesquite (e.g., Cartographer) are organized into their own Eclipse source code projects. If you have access to some of these projects, you can also check them out from the Mesquite GitHub repositories using the same mechanism described above. You will need to find the URI for the repository. For some of the repositories, you can explore on https://github.com/MesquiteProject/ For Cartographer, the URI is https://github.com/MesquiteProject/Cartographer.
    classPathsConfiguring Mesquite to load other projects
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    is as follows:follows for MacOS X and Linux:
    ../../Cartographer/Mesquite_Folder
    This(For Windows, use \ rather than /) This tells Mesquite
    If you have other projects that you want Mesquite to find, add more lines. For example, if you have a separate project called MyProject, then the classpaths.txt file would look like this:
    ../../Cartographer/Mesquite_Folder
    (view changes)
    10:01 pm

Saturday, December 30

  1. page Source Code edited ... Mesquite packages that are distributed separately from Mesquite (e.g., Cartographer) are organ…
    ...
    Mesquite packages that are distributed separately from Mesquite (e.g., Cartographer) are organized into their own Eclipse source code projects. If you have access to some of these projects, you can also check them out from the Mesquite GitHub repositories using the same mechanism described above. You will need to find the URI for the repository. For some of the repositories, you can explore on https://github.com/MesquiteProject/ For Cartographer, the URI is https://github.com/MesquiteProject/Cartographer.
    classPathsConfiguring Mesquite to load other projects
    ...
    is as follows.follows:
    ../../Cartographer/Mesquite_Folder
    This tells Mesquite to look outside of Mesquite_Folder, outside of MesquiteCore, then inside Cartographer/Mesquite_Folder. An example classpaths.txt file, as shown above, is contained in the Additional Files folder within the MesquiteCore folder in your workspace.
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    ../../MyProject/Mesquite_Folder
    It is also advisable to save a backup copy of your classpaths.txt file in another directory notunder subversion control. When updating Mesquite Project, the classpaths.txt file is sometimes deleted, so a backup copy would allow you to copy and paste the file into the Mesquite_Folder directory as opposed to creating a new classpaths.txt file every time you update your workspace.
    Note: in Mesquite 3.31 and earlier a classpaths.xml file was used to house extra classpaths. This was changed to the simpler text file format shown above in version 3.4 of Mesquite.
    updatingUpdating the latest source
    Once you have your Eclipse workspace configured, you can update your source code to the latest that is present on GitHub. To do this,
    (view changes)
    9:08 pm
  2. page Source Code edited ... The Mesquite application won't start up at all. To fix this, unzip the file executables.zip th…
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    The Mesquite application won't start up at all. To fix this, unzip the file executables.zip that is contained in the Additional Files folder, and move its contents into Mesquite_Folder, replacing the existing files of the same name. On Windows, if there is no Mesquite.exe in the Mesquite_Folder, then go in to the Additional Files folder, copy the Mesquite.exe file, and paste it into Mesquite_Folder.
    The Mesquite application will start up, but it will not complete the startup process because of an error. The message given is only "Error caught in Mesquite", or something equally cryptic. Check to see if there is a jars folder in Mesquite_Folder. There may be a jars folder in Mesquite Core (outside of the Mesquite_Folder), and copying that into Mesquite_Folder may work. However, if you still encounter problems, then unzip the jars.zip file that is Additional Files, and move the jars folder that is created into the Mesquite_Folder in the Mesquite Core folder.
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    away your classpaths.xmlclasspaths.txt file (see
    otherProjectsChecking out source for other projects
    Mesquite packages that are distributed separately from Mesquite (e.g., Cartographer) are organized into their own Eclipse source code projects. If you have access to some of these projects, you can also check them out from the Mesquite GitHub repositories using the same mechanism described above. You will need to find the URI for the repository. For some of the repositories, you can explore on https://github.com/MesquiteProject/ For Cartographer, the URI is https://github.com/MesquiteProject/Cartographer.
    classPathsConfiguring Mesquite to load other projects
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    creating a "classpaths.xml""classpaths.txt" file that
    ...
    of the classpaths.xmlclasspaths.txt file is as follows.
    <?xml version="1.0"?>
    <mesquite>
    <classpath>../../Cartographer/Mesquite_Folder</classpath>
    </mesquite>

    ../../Cartographer/Mesquite_Folder

    This tells
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    An example classpaths.xmlclasspaths.txt file, as
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    add more <classpath></classpath> lines. For
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    then the classpaths.xmlclasspaths.txt file would
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    like this:
    <?xml version="1.0"?>
    <mesquite>
    <classpath>../../Cartographer/Mesquite_Folder</classpath>
    <classpath>../../MyProject/Mesquite_Folder</classpath>
    </mesquite>

    ../../Cartographer/Mesquite_Folder
    ../../MyProject/Mesquite_Folder

    It is
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    of your classpaths.xmlclasspaths.txt file in
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    Project, the classpaths.xmlclasspaths.txt file is
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    a new classpaths.xmlclasspaths.txt file every
    updatingUpdating the latest source
    Once you have your Eclipse workspace configured, you can update your source code to the latest that is present on GitHub. To do this,
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    Right-click on the "Source" folder, select the "New" menu then choose "Package" in the "New" menu. In the name field, start your package name with "mesquite." and finish it with whatever the name of your Mesquite feature will be. Click "Finish" to create your new package.
    You can start creating new packages and classes underneath your new package as described in the developer's documentation. We also encourage you to use existing modules as models. Remember that for a module with class name MyModule to be found by Mesquite, its immediate package needs to have the same name (i.e., the module needs to be mesquite.mypackage.MyModule.MyModule.class).
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    edit the classpaths.xmlclasspaths.txt file located
    changingOfficialContributing changes to the official Mesquite code
    If you check out the MesquiteCore from the Mesquite repository, you will have Mesquite's main code base. You can make changes to this core code, if you wish. It may be the case that as you write your own modules, you will discover bugs in the main Mesquite code that need to be fixed or you will have methods that you would like to add to some of the standard classes such as DNAData. If you wish for us to consider incorporation of this code, then please submit a pull request in GitHub; please provide enough descriptive details in the pull request to help us judge the value of your modifications. If you wish to be involved more extensively, please contact us directly.
    (view changes)
    9:06 pm
  3. page Source Code edited ... Unzip the jars.zip file. Move the jars folder that is created into the Mesquite Folder in the…
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    Unzip the jars.zip file.
    Move the jars folder that is created into the Mesquite Folder in the Mesquite Core folder.
    ...
    edit a classpaths.xmlclasspaths.txt file so
    On Windows, if there is no Mesquite.exe in the Mesquite_Folder, then go in to the Additional Files folder, copy the Mesquite.exe file, and paste it into Mesquite_Folder.
    wontstartMy copy of Mesquite won't start or is missing features; why?
    (view changes)
    9:03 pm
  4. page home edited ... Current release version: 3.31 [download] If you have a previous version, please update becaus…
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    Current release version: 3.31 [download]
    If you have a previous version, please update because of bug fixes and new features.
    ...
    fix for this.this, and should release it in early January. In the
    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)
    9:00 pm
  5. page Source Code edited ... There are three different versions of the Mesquite source code available publicly: source cod…
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    There are three different versions of the Mesquite source code available publicly:
    source code of the official release versions of Mesquite. These are the simple, numbered versions (e.g., version 1.0, or version 3.0).
    ...
    quality to be generally useable.
    the current, active code that is in development. This active code is less well tested, and may contain more bugs and incomplete features, but it does contain new features and may also have some bug fixes.
    This page contains details on acquiring the source code, and developing your own code.
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    obtainingObtaining source code
    The Mesquite source is available via a version control system called GIT. There are many ways of accessing a GIT repository; we use the GIT plugin that is distributed with Eclipse. To begin, you will need to go to GitHub and create your own account.
    ...
    is present at the followingon GitHub URIs:in several versions:
    source code for the official releases can be found be exploring here: https://github.com/MesquiteProject/MesquiteArchive/tree/master/releases If you wish to pull down one of these versions, you should go there and find the version you want, so that you have the URL for that particular version.
    source code for the current interim release is the master branch at this URL: https://github.com/MesquiteProject/MesquiteCore.
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    URL: https://github.com/MesquiteProject/MesquiteCore. This branch normally is a functional version of Mesquite, but on occasion it may have notable issues.
    There will be other branches in the GitHub repository containing exploratory code that should in general not be trusted.

    In Eclipse, do the following steps to pull the Mesquite source code onto your computer:
    First, prepare Eclipse for the Mesquite code by choosing Preferences. In the Preferences dialog box, choose General, and then from within there touch on "Workspace". Under "Text file encoding", select "UTF-8" beside "Other". Press the Apply button, and then press OK to close the Preferences dialog box.
    (view changes)
    1:37 pm
  6. page Source Code edited ... Software distributed with and used by Mesquite Mesquite uses the following pieces of software…
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    Software distributed with and used by Mesquite
    Mesquite uses the following pieces of software:
    BrowserLauncher by Eric Albert
    ByteBuddy, distributed under an Apache 2.0 license.
    BrowserLauncher by Eric Albert
    corejava.Format by Horstmann & Cornell
    iText by Lowagie & Soares.
    JAMA by The MathWorks and NIST
    JSci by Mark Hale, Jaco van Kooten and others (see Mesquite source code for details).
    The PAL library by Drummond and Strimmer is used by the GTR substitution model for DNA sequence simulations.

    Mesquite Source Code License
    Mesquite source code is Copyright ©1997-2017 W.P. Maddison and D.R. Maddison unless otherwise stated in a source code file itself. Mesquite is distributed under the terms of the GNU Lesser General Public Licence. The example data files ARE NOT distributed under the GNU LGPL.
    (view changes)
    12:44 pm

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