Useful resources

-Compiled by Jer-Ming Hu

Web resources for molecular evolution

Here are some links of tools in molecular evolution related websites that I have used and recommended.

Category
Programs
Description

Compilation of many softwares

 Phylogenetic resources UC Berkeley, USA

Phylogeny programs University of Washington, USA

Sequence alignment

 CLUSTALW Thompson

A web-based version can be found here (hosted by EMBL-EBI).

RevTrans 1.4 server Center for Biological sequence analysis, Technical University of Denmark (DTU)

DataPartition A tool to remove user-defined columns from an alignment. It was originally used to decrease noise in phylogenetic signal by removing the fastest evolving sites from the data set.

Codon usage

 Codon Usage Database (Mainteined by) Yasukazu Nakamura (The First Laboratory for Plant Gene Research, Kazusa DNA Research Institute)

An extended WWW version of CUTG (Codon Usage Tabulated from GenBank) (Nakamura et al. 2000)

Codonw Correspondence Analysis of Codon Usage

John Peden

The project is hosted at SourceForge with lots of documentations

The link on the left is via PISE at the pasteur

Phylogenetic analysis

 PAUP*4.0 David Swofford

Florida State University

PAUPRat A tool to implement parsimony and likelihood ratchet searches using PAUP*

Derek S. Sikes and Paul O. Lewis (Department of Ecology and Evolutionary Biology, University of Connecticut)

PHYLIP the PHYLogeny Inference Package

Joe Felsenstein

A web server version is hosted by the Institut Pasteur, Paris.

BAMBE Bayesian Analysis in Molecular Biology and Evolution

B. Larget and D. Simon

A web-based tool.

MrBayes MrBayes is a program for the Bayesian estimation of phylogeny

John Huelsenbeck, Bret Larget, Paul van der Mark, and Fredrik Ronquist

PRAP Parsimony ratchet analyses with PAUP*, including random addition cycles of the ratchet and calculation of Bremer support applying the ratchet

Kai Müller (Nees-Institut für Biodiversität der Pflanzen, Meckenheimer, Germany)

He has also serveral phylogenetic softwares to download.

PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. (Link on the left is the direct link to the PhyML Online website)

Guindon S, Gascuel O. Systematic Biology. 2003 52(5): 696-704

Another online version is available on the Institut Pasteur, Paris.

Tree browsing

 MacClade 4 David R. Maddison (University of Arizona) and Wayne P. Maddison (University of British Columbia)

An interactive environment for exploring phylogeny (Maddison & Maddison 2002).

Mesquite Wayne P. Maddison (University of British Columbia) and David R. Maddison (University of Arizona)

A modular system for evolutionary analysis. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

Tree comparison

 Phylogeny Comparison Tom M.W. Nye (School of Mathematics and Statistics, University of Newcastle-upon-Tyne, UK)

A web-based java applet for comparing phylogenies (Nye et al. 2006).

TreeMap 2.0 Michael A. Charleston (Department of Zoology, University of Oxford) and Roderic D. M. Page (Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Science, University of Glasgow, UK)

A program designed for comparing host and parasite phylogenies (Charleston 1998; Page & Charleston 1998)

Hypothesis testing

 HyPhy Sergei L. Kosakovsky Pond, Spencer V. Muse, and Simon D. W. Frost

A free multiplatform software package for maximum likelihood analyses of hypothesis testing on sequence data (Kosakovsky Pond et al. 2005)

PAML Ziheng Yang (Department of Biology, University College London)

Phylogenetic analyses of DNA or protein sequences using maximum likelihood, especially on detecting selection pressure.

Executables are available for MS Windows and ANSI C source codes are distributed for UNIX/Linux/MacOSX

Model testing

 Modeltest David Posada and Keith Crandall

Comparing substitution models that is best for further analysis.

A web server version, FindModel, is developed by HCV Sequence Database Group.

Phylogenomics

 FlowerPower Berkeley Phylogenomics Group

FlowerPower is a protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences. More information here.

SHOT Shared Ortholog and Gene Order Tree Reconstruction Tool

Korbel, J. O., B. Snel, M. A. Huynen, and P. Bork (EMBL)

Shot is a (JavaScript) web-based tool for the reconstruction of genome phylogenies. See the documentation for more information.

Detecting recombination

 List of links A list of links to Recombination sequence Analysis / detection Programs

David Robertson

Discussion forum

 Genetic Software Forum A discussion forum for softwares on phylogenetic inference (e.g. MrBayes, PAML, etc.) and population genetics (e.g. Arlequin, BayesAss, DMLE+, GeneArtisan, Immanc, etc.), maintained by Bruce Rannala at UC Davis.

Teaching materials

Category
Places
Host

Botany

 Angiosperm Phylogeny Website Missouri Botanic Garden
Angiosperm DELTA L. Watson & M. J. Dallwitz

Australia
Digital Flowers Stephen R. Downie and Kenneth R. Robertson

Courseware for Plant Systematics (IB335) at the University of Illinois at Urbana/Champaign, USA
Flowering Plants Gateway Hugh D. Wilson

Bioinformatics working group, Texas A & M University, USA
NCBI Taxonomy homepage NCBI, USA
Vascular Plant Families Geral Carr

Botany Department, University of Hawaii at Manoa, USA
Wayne's Word Wayne P. Armstrong (Life Sciences, Palomar College, USA)

A great resource for botanical trivia, stories, etc.

Evolution

 National Center for Science Education This is a site dedicated to defending the teaching of evolution in the public school.

Other useful tools

Category
Programs
Description

Protein thesaurus

 BioThesaurus Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, and Cathy Wu

A web-based thesaurus of protein and gene names (Liu et al. 2006)

References

APG. 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85(4): 531-553.

Bremer, B., Bremer, K., Chase, M.W., Reveal, J.L., Soltis, D.E., Soltis, P.S., Stevens, P.F., Anderberg, A.A., Fay, M.F., Goldblatt, P., Judd, W.S., Kallersjo, M., Karehed, J., Kron, K.A., Lundberg, J., Nickrent, D.L., Olmstead, R.G., Oxelman, B., Pires, J.C., Rodman, J.E., Rudall, P.J., Savolainen, V., Sytsma, K.J., van der Bank, M., Wurdack, K., Xiang, J.Q.Y., and Zmarzty, S. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141(4): 399-436.

Charleston, M. A. 1998. Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149:191-223.

Korbel, J. O., B. Snel, M. A. Huynen, and P. Bork. 2002. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics 18:158-162. [PubMed]

Kosakovsky Pond, S. L., S. D. W. Frost and S.V. Muse. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679 [PubMed]

Larget, B. and D. Simon 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16:750-759.

Liu, H., Z.-Z. Hu, J. Zhang, and C. Wu. 2006. BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics 22: 103-105. [PubMed]

Nakamura, Y., T. Gojobori, and T. Ikemura. 2000. Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Research 28: 292.

Nye, T. M. W., P. Lio, and W. R. Gilks. 2006. A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 22:117-119. [PubMed]

Page, R. D. M. and Charleston, M. A. 1998. Trees within trees: phylogeny and historical associations. Trends in Ecology and Evolution 13(9):356-359.

Maintained by Jer-Ming Hu [EMAIL: jmhu@ntu.edu.tw]