softlinks.amnh.org
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/popgen.html
A program for Bayesian MCMC analysis of molecular sequences. Orientated towards molecular clock analyses. Not for constructing phylogenies but rather testing evolutionary hypotheses without preconditioning on a single tree topology. Uses MCMC to average over tree space, so that each tree is weighted proportionally to its posterior probability. Implements a Bayesian generalized skyline plot. Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined.
mbe.oxfordjournals.org
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
http://mbe.oxfordjournals.org/content/29/8/1969
Molecular Biology and Evolution. View Current Issue (Volume 33 Issue 9 September 2016). Molecular Biology and Evolution. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Alexei J. Drummond. Marc A. Suchard. Department of Computer Science, University of Auckland, Auckland, New Zealand. Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand. Department of Biostatistics, School of Public Health, University of California, Los Angeles. Alert me when cited.
phylo.org
Portal | CIPRES
http://www.phylo.org/index.php
The TSCC resource at CIPRES will undergo maintenance for 24 hours, Tuesday, 8/30/2016 07:00 AM Pacific time. TSCC Jobs (all serial jobs) that enter the maintenance period will be held in the queue until maintenance is complete. We regret any inconvenience. The CIPRES Science Gateway V. 3.3. The CIPRES Science Gateway V. 3.3. Is a public resource for inference of large phylogenetic trees. It is designed to provide all researchers with access to NSF XSEDE. If you need access to PhyloBayes.
epidemic.bio.ed.ac.uk
MERS-Coronavirus Molecular Epidemiology and Genetic Analysis - Origin and Evolution | epidemic
http://epidemic.bio.ed.ac.uk/coronavirus_analysis
Skip to main content. Molecular Epidemiology and Evolution of Viral Pathogens. MERS-Coronavirus Molecular Epidemiology and Genetic Analysis - Origin and Evolution. MERS-Coronavirus Molecular Epidemiology and Genetic Analysis - Origin and Evolution. Submitted by Andrew Rambaut. On Fri, 2013-06-14 10:26. MERS-Coronavirus Molecular Epidemiology and Genetic Analysis. This is an update of an older page describing an analysis based on 13 sequences, here. Or Cotten et al 2014. Maximum likelihood phylogeny of co...
julieaherman.com
Resources | The Great Plant Science Adventure
https://julieaherman.com/resources
The Great Plant Science Adventure. Diversity, defense, and speciation. Many of these can be used to kickstart independent data mining projects! Repository of many phylogenetic trees and large datasets that have been published. Repository of most if not all genetic sequences referred to in publications. An aggregator for sequences by taxonomic classification and locus. Genes and information on biosynthetic pathways. A tool for putting dates on/calibrating phylogenetic trees. A phylogenetic tree viewer.
justinbagley.org
Collaborators - Justin C. Bagley - Postdoctoral Researcher
http://www.justinbagley.org/collaborators
Justin C. Bagley – Postdoctoral Researcher. UnB Dept. de Zoologia. Scientific Presentations: Posters and Talks. Research Advice & Resources. General Ecology – BIOL 3700. Topics in Zoology: Integrative Taxonomy – ZOO 397806. Merging ecology, evolution, and historical biogeography. You are here :. Justin C. Bagley - Postdoctoral Researcher. November 14, 2013. Brigham Young University (Provo, UT, U.S.A.). City University of New York (New York, NY, U.S.A.). Frost Science Museum (Miami, FL, U.S.A.). Jerry and...
treegraph.bioinfweb.info
Open files - TreeGraph help
http://treegraph.bioinfweb.info/Help/wiki/Open_files
Help - Open files. The option " Open. In the file menu. Displays a dialog that can either be used to open TreeGraph 2 tree files (*.xtg) or to import other supported tree formats (e.g. Nexus). You can select any file in a supported format here to open it in the TreeGraph 2 editor. This article describes this feature for the latest version of TreeGraph 2. For older versions the following articles are available:. Open files (until 2.0.34). XTG before version 2.0.40. Nexus format with additional annotations.
gavinhthomas.wordpress.com
Blog | gavinhthomas | macroevolution: tempo and mode
https://gavinhthomas.wordpress.com/blog
Macroevolution: tempo and mode. Skip to primary content. Skip to secondary content. October 16, 2013. The trait MEDUSA (tm1 and tm2) methods in previous versions of MOTMOT have a bug. The AIC and AICc values are incorrect due to a miscounting of the number of parameters in the model. This will affect choice among models and specifically may result in the choice of over-parameterised models. The corrected code is now on github. Thanks to Graham Slater for spotting this bug. April 5, 2013. Regular users of...
gavinhthomas.wordpress.com
Polytomy resolver problems | gavinhthomas
https://gavinhthomas.wordpress.com/2013/04/05/polytomy-resolver-problems
Macroevolution: tempo and mode. Skip to primary content. April 5, 2013. Since the paper on resolving polytomies in phylogenetic trees ( Kuhn et al 2011. Was published in MEE. I have received occasional reports of problems running the output of our polytomy resolver code in BEAST. The error message invariably includes the following:. The initial model is invalid because state has a zero probability. And the issues with the polytomy resolver script appear to apply from version 1.6.x upwards. It...The error...
