PRAP (Parsimony and likelihood ratchet analyses with PAUP*) 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.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.
MrModeltest is a modified version of David Posada’s Modeltest. “Modified version” means that it was rewritten to compare 24 instead of 56 models of nucleotide substitution (basically a Modeltest version 1.0). On the other hand, all of the 24 models can be implemented in MrBayes version 3. Furthermore, MrModeltest uses (by default) four different hierarchies for the likelihood ratio tests.
PaupUp is developped to provide a user-friendly interface to the phylogenetic program PAUP* on Windows operating systems. The DOS version of PAUP* is entirely command-line driven and does not provide any graphical interface. PaupUp partly resolves this issue, providing around 80% of the available commands (the most commonly used in our opinion) in a graphical environment comparable to the MAC OS version while the last 20% commands are still available through direct command-line input in a single integrated design.
txgen generates a script for PAUP*, to calculate MP or ML tree scores on a sliding window of nucleotide data given an input tree. The program also parses PAUP*’s log file into a table that can be used in your favourite spreadsheet.
WINIPAUP (Windows Interface for PAUP) is an interface allowing the creation of NEXUS files including the data and the commands necessary to the realization of analyzes in PAUP software (D. SWOFFORD).WINIPAUP allows the importation of sequences (nucleotidic and proteic), discrete data, distances matrix, phylogenetic trees and NEXUS files.Moreover the software allows the creation of files which, carried out in PAUP, provide results files usable by MODELTEST software (D. POSADA).