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If you want to use TreeConverge to conduct an automated iterative ML searched, please
cite: Sullivan, J. Sullivan, J., Z. Abdo, P. Joyce, and D. L. Swofford. 2005.
Evaluating the performance of a successive-approximations approach to parameter
optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution,
22:1386-1392. (Download a PDF).
Download User's Manual
You'll need to install Perl to run the script. If you have
a Mac and are running OS X, you're all set.
Using topology and branch lengths in assessing convergence:
TreeConverge script (Save as a text file called
tree_converge.pl)
Initial tree generation (Save as a
text file called Model_Command_Initial_Tree.)
Code for TreeConverge (Save as a text file
called Model_Command_Iter_Trees.)
Using Symmetric-Difference Distance to determine convergence
TreeConvergeSDD (Save as a text file
called tree_converge_symDist.pl)
Download library
Initial tree generation (Save as a
text file called Model_Command_Initial_Tree.)
Code for TreeConverge (Save as a text file
called Model_Command_Iter_Trees.)
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