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MorphoBank and CIPRES
We are happy to announce that MorphoBank has partnered with CIPRES (Cyberinrastructure for Phylogenetic Research) to allow users to run a matrix and search for a tree (or trees) using the Parsimony Ratchet. The Parsimony Ratchet improves your ability to find shortest trees during heuristic searches on datasets. You will be able to run your matrix on the Web by sending it to the online algorithms at CIPRES. There are several settings you must define from within your MorphoBank project for the process to work. First, you will need to create a name for the job and add any helpful notes. Then, you will need to set parameters. Choose a Branch-swapping Algorithm to inform a heuristic search for a starting tree. Then PAUP will perform two searches for each of whatever number of iterations you specify. In the first search a subset of your characters will be assigned a weight of 2, and in the second all characters will be equally weighted. You must choose the number or percent of characters to permute. After your chosen number of iterations, CIPRES will return the resulting file to the MorphoBank Matrices page. Your underlying matrix will remain unchanged. A link to the CIPRES portal is provided below for additional reference.
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