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  1. page History of New Features edited ... Parsimony analyses can now be done with meristic data matrices, using Linear Parsimony (analog…
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    Parsimony analyses can now be done with meristic data matrices, using Linear Parsimony (analogous to Ordered parsimony with categorical data).
    There is a new tree source, Concatenate Multiple Tree Sources, that brings together several tree sources into one.
    NewRerootedInformationNew options have
    The reporting of crashes and checksum errors has been improved.
    Bug Fixes
    (view changes)
    3:15 pm
  2. page History of New Features edited ... You can now assign different bin boundaries and colors when using continuous characters in Tra…
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    You can now assign different bin boundaries and colors when using continuous characters in Trace Character History. By default there are 11 bins of fixed widths for the shading of the character states, and the colors are either a pre-defined spectrum or grayscale. Now, you can use Set Number of Bins in the Trace menu to change the number of bins, and Set Bin Boundaries to change bin boundaries. To change colors used, double click on the color rectangles in the legend for Trace Character History and choose the new color. These binnings are specific to a given Tree window. The colors are specific to a given Tree window unless you choose Set Custom Colors as Defaults.
    If you have a tree whose stored branch lengths represent not branch lengths but divergence times, then you can ask Mesquite to reinterpret these numbers so as to assign actual branch lengths, using "Branch Lengths from current, reinterpreted as Divergence Times" in the Tree Window's Alter/Transform Branch Lengths submenu. Thus, if a node had "50.4" as branch length but in fact that was a divergence time, and its immediate ancestral node was assigned "56.7", also a divergence time, then if you used "Branch Lengths from current, reinterpreted as Divergence Times" the node's branch length would be reassigned as 6.3 (= 56.7 - 50.4). This function can be useful if you are importing trees from a program such as TreeAnnotator that assigns divergence times based on BEAST runs. (See item below for a scenario of how this would be used.)
    IfNumbersAtNodesIf you have
    ...
    be used.)
    Reading

    ImportInformationAtNodesReading
    of trees
    Prepare the tree file from TreeAnnotator by replacing & to % in the comments in the tree descriptions, then read the file with Mesquite.
    In the tree window, show the tree of interest. Select Obtain Branch Lengths from Values Attached to Nodes from the Alter/Transform Branch Lengths submenu, and select the divergence time you want to use (e.g., height or height_median). This will transfer these divergence times into the branch lengths of the tree. The problem with this is that, of course, divergence times are not the same as branch lengths. So, you need to ask Mesquite to recalculate the branch lengths.
    (view changes)
    12:08 pm

Wednesday, June 7

Monday, June 5

Monday, May 22

  1. page History of New Features edited ... Drawing of coalescent trees contained within another tree was broken in version 3.1. Fixed in …
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    Drawing of coalescent trees contained within another tree was broken in version 3.1. Fixed in Build 809.
    Separated suppression of TITLE and LINKs commands from suppression of ID and BLOCKID commands for better compatibility with PAUP*. Build 811.
    Fused Matrix Export (NEXUS) wrote incorrect FORMAT statements. Fixed in Build 828.
    Version 3.2
    New Features
    (view changes)
    8:20 am

Monday, March 6

  1. page History of New Features edited ... A bug was introduced in Mesquite 3.2 that changes how taxon names were simplified; in particul…
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    A bug was introduced in Mesquite 3.2 that changes how taxon names were simplified; in particular, in various contexts in which underscores should have been used in taxon names, they were removed. This may cause various file incompatibilities, and would alter the behavior of Simplify Taxon Names. Fixed in Build 807.
    Drawing of coalescent trees contained within another tree was broken in version 3.1. Fixed in Build 809.
    Separated suppression of TITLE and LINKs commands from suppression of ID and BLOCKID commands for better compatibility with PAUP*. Build 811.
    Version 3.2
    New Features
    (view changes)
    5:18 pm
  2. page History of New Features edited ... NCBI changed how BLAST searches are conducted programmatically, and Mesquite's Matrix > Sea…
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    NCBI changed how BLAST searches are conducted programmatically, and Mesquite's Matrix > Search > Top BLAST Matches on the NCBI server failed as a result. Fixed in Build 803.
    A bug was introduced in Mesquite 3.2 that changes how taxon names were simplified; in particular, in various contexts in which underscores should have been used in taxon names, they were removed. This may cause various file incompatibilities, and would alter the behavior of Simplify Taxon Names. Fixed in Build 807.
    Drawing of coalescent trees contained within another tree was broken in version 3.1. Fixed in Build 809.
    Version 3.2
    New Features
    (view changes)
    12:59 pm

Sunday, February 12

  1. page History of New Features edited ... Bug Fixes and Workarounds NCBI changed how BLAST searches are conducted programmatically, and…
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    Bug Fixes and Workarounds
    NCBI changed how BLAST searches are conducted programmatically, and Mesquite's Matrix > Search > Top BLAST Matches on the NCBI server failed as a result. Fixed in Build 803.
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    introduced in simplifyingMesquite 3.2 that changes how taxon names that wouldwere simplified; in particular, in various contexts in which underscores should have been used in taxon names, they were removed. This may cause various
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    Taxon Names. Fixed in Build 807.
    Version 3.2
    New Features
    (view changes)
    12:19 pm
  2. page History of New Features edited ... Bug Fixes and Workarounds NCBI changed how BLAST searches are conducted programmatically, and…
    ...
    Bug Fixes and Workarounds
    NCBI changed how BLAST searches are conducted programmatically, and Mesquite's Matrix > Search > Top BLAST Matches on the NCBI server failed as a result. Fixed in Build 803.
    A bug was introduced in simplifying taxon names that would cause various file incompatibilities, and would alter the behavior of Simplify Taxon Names.
    Version 3.2
    New Features
    (view changes)
    12:15 pm

Saturday, January 28

  1. page History of New Features edited ... Features in the next release version of Mesquite; the latest source code in the development br…
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    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
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    be needed. Build 805.
    Bug Fixes and Workarounds
    NCBI changed how BLAST searches are conducted programmatically, and Mesquite's Matrix > Search > Top BLAST Matches on the NCBI server failed as a result. Fixed in Build 803.
    (view changes)
    12:10 pm

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