FeaturesDownloadsSupportMacCladeis a computer program for phylogenetic analysis written by DavidMaddison and Wayne Maddison. Its analytical strength is in studiesof character evolution. It also provides many tools for enteringand editing data and phylogenies, and for producing tree diagramsand charts.MacClade will not work under MacOS 10.7 (Lion)Apple is dropping support for older programs like MacClade in the next version of their operating system, MacOS 10.7 (codenamed 'Lion'), which is expected to be released summer 2011.Thus, MacClade will not work on machines with that operating system installed. If you are using MacOS 10.7, we suggest you explore instead. MacClade is now available as a free downloadAs of 1 May 2011, MacClade is no longer being distributed by Sinauer Associates, and is now freely available from this site's page.
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Thanks to Sinauer AssociatesFor 19 years, Sinauer Associates have been the publishers of MacClade, beginning with version 3.0, and ending on 30 April 2011, with version 4.08. During this time they have been the epitome of a superb publisher: professional, thoughtful, considerate, generous, flexible, and focused on quality. In today’s world, with the ease of inexpensive Internet distribution, they have been the perfect example of the continuing value of a for-profit publisher, and what a dedicated group of capable individuals can do.
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For Mac, Paup operates via the Terminal interface – the command-line system that “hides” behind the icon-driven desktop you normally use. If you double-click the PAUP icon you will automatically open and run PAUP in this interface, However, you can also open this interface first and then run PAUP.
We are deeply thankful to Andy Sinauer, Dean Scudder, and all who work at Sinauer Associates, for everything that they have done for us. MacClade and the new Intel MacsMacClade apparently runs fine on the new Intel Macs, and under thenewer operating systems up to MacOS 10.6; we have not encountered problems, norhave we heard of any problems. If any of you encounter problems,please contact us. (MacClade has not yet been rebuilt to runnativelyonthenewIntelMacs, but that should not matter.)MacClade 4.08 is availableMacClade 4.08 is available, including a version forMacOS X. It has a number of new tools, includingsome for sequence alignment. Check out thepage for more information.MacClade 4's tree window in MacOS XMacClade 4's data editor in MacOS X.Features.; thispage gives information about a few of MacClade 4's novel features.Downloads.Support.If you have MacClade 3, but not MacClade 4, and wish to see bugreports, updates to version 3.08, etc., see:.Copyright ©2011 by David R.
Maddison and Wayne P. Maddison.All rights reserved.
Jmodeltest2jModelTest 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.DownloadCheck 'releases' section for the latest distributions.New revisions of jModelTest will also be hosted in google drive:NEWS!
- New revision fixed bug with equal taxa name prefixes. Fixed minor bugs.
New revision Fixed minor bug in console version. NNI tree search operation was taken as default for ML starting tree, instead of BEST. New revision Fixed some bugs with Windows OS - New revision Added -set-local-config and -set-property arguments. New revision Fixed bug with -O argument (hypothesis order for hLRT). New revision Added checkpointing feature and confirmation on run cancel. New revision Added PAUP. block to log files.
Fixed bug with DT criterion. Check the whole revision updates at the wiki. New revision Fixed bug with PAUP. block.
Added argument for forwarding standard output to a file. New revision Fixed bug with paths including whitespaces. New binaries distribution also includes updated PhyML binaries with a much better performance. The jModelTest paper has been published: Darriba D, Taboada GL, Doallo R, Posada D. 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!CitationWhen using jModelTest you should cite all these:Darriba D, Taboada GL, Doallo R, Posada D. 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 groupPlease use the jModelTest discussion group for any question:DisclaimerThis 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, 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.
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