Recent Changes

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…
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    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
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    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…
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    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
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    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
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    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 …
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    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
  5. page History of New Features edited ... New Features A new tool has been added to the data matrix window for non-molecular categorica…
    ...
    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.
    The number of items in the project panel is limited to save memory and time. The default of 50 can now be changed under File>Defaults>Maximum # Items in Project Panel....
    Bug Fixes and Workarounds
    Mesquite (as of build 875) can now
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    Java 9. Build 875.This required building a new startup protocol to accommodate Java 9 changes and restrictions.
    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.
    (view changes)
    11:22 am

Friday, January 26

  1. 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.
    ...
    it in early January. In
    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)
    8:08 pm

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