Paup Free Download For Mac

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implemented parsimony, but from version 4.0 (when the program became known as PAUP*) it also supports distance matrix and likelihood methods. Version 3.0 ran on Macintosh computers and supported a rich, user-friendly graphical interface. Together with the program MacClade,^[1] with which it shares the NEXUS data format,^[2] PAUP* was the phylogenetic software of choice for many phylogenetists.^[3] Version 4.0 added support for Windows (graphical shell and command line) and Unix (command line only) platforms. However, the graphical user interface for the Macintosh version requires Classic, which is no longer supported by Mac OS X 10.5 and later. There is a command line version of PAUP* for Intel-based Macs. PAUP* is also available as a plugin for Geneious. The program now sports the self-referential title of PAUP* (* Phylogenetic Analysis Using PAUP).

References[edit]

1. ^D R Maddison & W. P. Maddision (2001-02-08). MacClade 4: Analysis of Phylogeny and Character Evolution. ISBN0-8789-3470-7.
2. ^Maddison DR, Swofford DJ, Maddison WP (1997). 'NEXUS: an extensible file format for systematic information'. Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. ISSN1063-5157. PMID11975335.CS1 maint: uses authors parameter (link)
3. ^Hall, Barry G. (2001). Phylogenetic Trees Made Easy. Sinauer Associates. ISBN0-8789-3311-5.

Is included in the tutorial folder but is also available here as a free download. For Mac, Paup operates via the Terminal interface – the command-line system.

Minecraft alpha 1.2 6 full for mac. KeyActionLOpen the Advancements screenEscapePause, open the Options menuF1Hide the heads-up displayF2Take an in-game screenshotF3View the debug display to show the character's coordinates and other informationF4Disable shadersF5Toggle between first-person (default) and third-person perspectiveF6Toggle stream on/offF7Pause streamF8Improve mouse sensitivityF11Switch between full-screen and windowed displaysControl + BToggle the narrator on/offC + #Save the current toolbar to the specified numberX + #Load the specified tool bar.

External links[edit]

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch lenght), heuristic filtering and automatic logging of user activity.

Download

Check 'releases' section for the latest distributions.

New revisions of jModelTest will also be hosted in google drive: https://drive.google.com/folderview?id=0ByrkKOPtF_n_OUs3d0dNcnJPYXM#list

NEWS!

03/03/2016 - New revision fixed bug with equal taxa name prefixes. Fixed minor bugs.

20/02/2015 - New revision Fixed minor bug in console version. NNI tree search operation was taken as default for ML starting tree, instead of BEST.

20/11/2014 - New revision Fixed some bugs with Windows OS

03/09/2014 - New revision Added --set-local-config and --set-property arguments.

26/08/2014 - New revision Fixed bug with -O argument (hypothesis order for hLRT).

06/08/2014 - New revision Added checkpointing feature and confirmation on run cancel.

05/04/2014 - New revision Added PAUP* block to log files. Fixed bug with DT criterion. Check the whole revision updates at the wiki.

05/06/2013 - New revision Fixed bug with PAUP* block. Added argument for forwarding standard output to a file.

03/01/2013 - New revision Fixed bug with paths including whitespaces. New binaries distribution also includes updated PhyML binaries with a much better performance.

01/08/2012 - The jModelTest paper has been published: Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772. Although the main text is quite short, it comes with 15 pages of supplementary material!

Citation

When using jModelTest you should cite all these:

Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772.

Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood'. Systematic Biology 52: 696-704.

Discussion group

Please use the jModelTest discussion group for any question: http://groups.google.com/group/jmodeltest

Disclaimer

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. The jModelTest distribution includes Phyml executables.

These programs are protected by their own license and conditions, and using jModelTest implies agreeing with those conditions as well.