Parsimony and likelihood ratchet analyses with PAUP.

Functions of PRAP
1. PRAP allows the calculation of Bremer support (BS, Decay values; Bremer 1988) using the parsimony ratchet algorithm (Nixon, 1999). Alternatively, BS can also be computed without using the ratchet.
2. In addition, simple Parsimony Ratchet searches can be performed with PRAP, also by superposing random addition cycles onto the published ratchet procedure (Nixon, 1999) to further decrease the slight risk that even the Ratchet gets stuck in a single series of cycles. Here, a series of ratchet iterations (commonly about 200 iterations) is repeatedly started from different starting trees, and shortest trees from all these iterations series are collected.
3. Since version 2, likelihood ratchet searches are supported. The likelihood ratchet by Morrison (2007) can be loaded and, if desired, modified by the user.

How it works
1. PRAP reads NEXUS (Maddison et al., 1997) data and tree files supplied by the user.

2. For Decay analyses, PRAP creates constraint trees for each branch and writes commands for PAUP (Swofford, 1998) into a command file. Instead of simple heuristic search statements, a series of commands is written for each branch, corresponding to the parsimony ratchet procedure. The user can supply parameters influencing efficiency and search time of the ratchet. When executing this command file, PAUP* calculates MP trees using the reverse constraint option. A log file is created and parsed by PRAP to determine how much more steps a tree which constraints a given branch requires. This value, corresponding to the BS, is assigned to the branch. This is done for each branch in the tree. The whole tree and its BS values are finally written to a NEXUS tree file that can be viewed with the program TreeView (Page, 1996) or imported into TreeGraph (M ller & M ller 2004) for generating publication-ready tree figures.

3. For plain parsimony ratchet searches (without decay value calculation), a command file is created as well. Instead of simple heuristic search statements, a series of commands is written, corresponding to random addition cycles of individual parsimony ratchet searches. The same applies to likelihood ratchet searches.
What you have to do (it's obvious, so you might want to jump over the next points...):

Requirements:
* Java

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