Paup GUI 2011 – User-friendly Interface to Phylogenetic program PAUP*

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.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

PRAP

:: MORE INFORMATION

Citation

Müller K
The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support
BMC Evolutionary Biology 2005, 5:58

Mailfit 0.2 – Perl script that runs PAUP and MrModeltest2

Mailfit 0.2

:: DESCRIPTION

Mailfit is a Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail

::DEVELOPER

Johan Nylander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
Perl

:: DOWNLOAD

Mailfit

:: MORE INFORMATION

MrModeltest 2.3 – C program for selecting DNA substitution models using PAUP*

MrModeltest 2.3

:: DESCRIPTION

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.

::DEVELOPER

Johan Nylander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Linux/ MacOsX

:: DOWNLOAD

MrModeltest

:: MORE INFORMATION

PaupUp 1.0.3.1 – Graphical Frontend for Paup* DOS software

PaupUp 1.0.3.1

:: DESCRIPTION

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.

::DEVELOPER

Jean-Francois Martin at martinjf@supagro.inra.fr

:: SCREENSHOTS

:: REQUIREMENTS

Windows
PAUP*

:: DOWNLOAD

PaupUp

:: MORE INFORMATION

txgen 0.1 – PAUP Text Generator and Parser

txgen 0.1

:: DESCRIPTION

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.

::DEVELOPER

Dr. Philipp Schlüter

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

txgen

:: MORE INFORMATION

WinIPaup 1.0 – Windows Interface for PAUP to Create NEXUS Files

WinIPaup 1.0

:: DESCRIPTION

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).

::DEVELOPER

Daniel Montagnon PhD

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

WinIPaup

:: MORE INFORMATION

If you download and use this software please register to be informed for new release and modifications.

GRate 1.0 – Relative Rate Test for Groups of Taxa Using General DNA Substitution Models in PAUP*

GRate 1.0

:: DESCRIPTION

GRate is a software for relative rate tests with groups supporting all models of nucleotide substitution known by PAUP*.

::DEVELOPER

Kai Müller

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX

:: DOWNLOAD

GRate

:: MORE INFORMATION

Citation

Müller K, Borsch T, Legendre L, Porembski S, Theisen I, Barthlott W
Evolution of carnivory in Lentibulariaceae and the Lamiales
Plant Biology 2004, 6:477-490