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[Treebase-guts] SF.net SVN: treebase:[382] trunk/treebase-core/lib/mesquite
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From: <rv...@us...> - 2009-12-15 18:38:54
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Revision: 382
http://treebase.svn.sourceforge.net/treebase/?rev=382&view=rev
Author: rvos
Date: 2009-12-15 18:38:47 +0000 (Tue, 15 Dec 2009)
Log Message:
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Adding mesquite classes
Added Paths:
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trunk/treebase-core/lib/mesquite/ancstates/
trunk/treebase-core/lib/mesquite/ancstates/AncestralStatesAll/
trunk/treebase-core/lib/mesquite/ancstates/AncestralStatesAll/AncestralStatesAll.class
trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/
trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesDecorator.class
trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesOnTree.class
trunk/treebase-core/lib/mesquite/ancstates/RecAncestralStates/
trunk/treebase-core/lib/mesquite/ancstates/RecAncestralStates/RecAncestralStates.class
trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/
trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesDecorator.class
trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesOnTree.class
trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/
trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllCharacters.class
trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllOperator.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TCMPanel.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCOTOperator.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceLegend.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceModule.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/SpecsPrintTextArea.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TCMPanel.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterHistory.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterOperator.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceLegend.class
trunk/treebase-core/lib/mesquite/ancstates/UnambigChangesAtNodes/
trunk/treebase-core/lib/mesquite/ancstates/UnambigChangesAtNodes/UnambigChangesAtNodes.class
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/aAncStatesIntro.class
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/splash.gif
trunk/treebase-core/lib/mesquite/ancstates/explanation.txt
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--- trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html 2009-12-15 18:38:47 UTC (rev 382)
@@ -0,0 +1,124 @@
+<html>
+
+ <head>
+ <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+ <meta name="generator" content="Adobe GoLive 4">
+ <title>Parsimony</title>
+ </head>
+
+ <body>
+ <h2>
+ <table border="4" cellpadding="0" cellspacing="2">
+ <tr>
+ <td><img height="64" width="164" src="splash.gif"></td>
+ <td>
+ <h2>Ancestral State Reconstruction Packages for Mesquite</h2>
+ </td>
+ </tr>
+ </table>
+ </h2>
+ <h4>Wayne Maddison & David Maddison</h4>
+
+<p>August 2005, version 1.06.</p>
+ <ul>
+ <li><a href="#overview">Overview</a>
+ <li><a href="#modules">Modules</a>
+ <li><a href="#examples">Examples</a>
+ </ul>
+ <h3><a name="overview"></a>Overview</h3>
+
+<p>See the <a href="../../../docs/mesquite/CharacterEvolution/AncestralStates.html">manual
+ page on ancestral states</a> for an introduction on how to use Mesquite to
+ reconstruct ancestral states.</p>
+<p>Mesquite's standard packages include several that provide calculations to
+ reconstruct ancestral states on a phylogenetic tree. These are the "<strong>ancstates</strong>"
+ package, which coordinates the reconstruction, the "<strong>parsimony</strong>" package, which
+ reconstructs using parsimony methods, and the "<strong>stochchar</strong>" package, which reconstructs
+ using likelihood methods.</p>
+<h3><a name="modules"></a>Modules</h3>
+ <p>Some of the modules available in these packages are:</p>
+ <ul>
+ <li><strong>Ancstates package: </strong>
+ <ul>
+ <li><b>Trace Character History</b> -- Displays on a tree the reconstructed
+ ancestral states at each of the nodes.
+ </li>
+ <li><b>Trace All Characters</b> -- Summarizes reconstructed ancestral
+ states for a series of characters at each of many nodes. </li>
+ <li><b>Trace Character Over Trees</b> -- Summarizes reconstructed ancestral
+ states for a character on each of many trees. </li>
+ </ul>
+ <li><strong>Parsimony package</strong></li>
+ <ul>
+ <li><strong>Parsimony Ancestral States</strong> -- Reconstructs the
+ history of ancestral states in the character
+ given a tree and a character distribution, so as to minimize amount of
+ character change. </li>
+ <li><strong>Parsimony Character Steps</strong> -- Calculates the parsimony
+ steps in a character given a tree. </li>
+ <li><strong>Treelength</strong> -- Calculates the treelength of a tree
+ for a character matrix. The treelength is the weighted sum of
+ parsimony steps over
+ characters. </li>
+ <li><strong>Parsimony Unordered</strong> --
+ Calculates the most parsimonious ancestral states at the nodes
+ of the tree assuming one
+ step per state change (this assumption is known as unordered or Fitch parsimony).
+ Also calculates the number of steps in a most parsimonious reconstruction. </li>
+ <li><strong>Parsimony Ordered</strong> - Calculates the most parsimonious
+ ancestral states at the nodes of the tree assuming states are
+ ordered (this assumption
+ is known as ordered, Farris or Wagner parsimony). Also calculates the number
+ of steps in a most parsimonious reconstruction. </li>
+ <li><strong>Parsimony Cost Matrix</strong> - Calculates the most parsimonious
+ ancestral states assuming state changes cost the number of steps
+ indicated
+ in the states X states matrix. Known as Stepmatrix or Cost Matrix parsimony. </li>
+ <li><strong>Stepmatrix Curator</strong> - Provides window to edit
+ stepmatrices. </li>
+ <li><b>Parsimony Linear</b> -- Calculates the most parsimonious
+ ancestral states at the nodes of the tree assuming a cost of <font size="4"><b>|x-y|</b></font><b> </b>on
+ a branch if the branch shows a change from state x to state y
+ (this assumption is known as linear, Farris, or Wagner parsimony).
+ Also
+ calculates the cost of a most parsimonious reconstruction. </li>
+ <li><b>Parsimony Squared</b> -- Calculates the most parsimonious
+ ancestral states at the nodes of the tree assuming a cost of <font size="4"><b>(x-y)<sup>2</sup></b></font> on
+ a branch if the branch shows a change from state x to state y
+ (this assumption is known as squared change or least-squares parsimony).
+ Also calculates the cost of a most parsimonious reconstruction. </li>
+ </ul>
+ <li><strong>Stochchar package</strong></li>
+ <ul>
+ <li><strong>Likelihood Ancestral States</strong><strong></strong> --
+ Reconstructs the history of ancestral states in the character
+ given a tree and a character distribution, so as to maximize
+ the probability of evolving the observed states. </li>
+ <li><strong>Likelihood in Character</strong> -- Calculates the likelihood
+ of a tree for a single character.</li>
+ <li><strong>Mk Model Curator</strong> -- Provides a window to edit
+ Mk1 models of evolution.</li>
+ <li><strong>AsymmMk Model Curator</strong> -- Provides a window to
+ edit AsymmMk models of evolution. </li>
+ <li><strong>Mk1 Rate</strong> -- Calculates the rate of character
+ change under an Mk1 model of evolution.</li>
+ <li><strong>Asymmetry LR</strong> -- Calculates the test statistic
+ for the likelihood ratio test comparing the asymmetrical and
+ one parameter models [2ln(Likelihood(AsymmMk.)/Likelihood(Mk1)],
+ on a tree for a given character . </li>
+ </ul>
+ </ul>
+
+ <h3><a name="examples"></a>Examples</h3>
+
+<p>See the examples files in Mesquite_Folder/examples/Ancestral_States.</p>
+ <h3>
+ <p>
+ <hr>
+ </p>
+ </h3>
+
+<p>© Wayne Maddison & David Maddison, 2002-2005
+</body>
+
+</html>
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+Ancestral States Package
+One of the core Mesquite packages. Coordinates reconstruction and display of ancestral states of characters on phylogenetic trees. Includes "Trace Character History". To function, requires other packages such as the parsimony or likelihood packages to perform the reconstruction.
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