1. Sequence Editing and Alignment
2. Phylogenetics
3. Population Genetics
4. Microsatellite Fragment Analysis
Click on the name of the software to be taken to the software source site.
Sequencher: This is a commercial DNA sequence analysis software package. We use it primarily for editing raw sequence chromatograms and exporting edited and aligned sequences to other programs. It is extremely expensive (in excess of $1000), but very good.
ClustalX: A free program written by Thompson et al. (1997) used for multiple sequence alignment.
Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24:4876-4882.
ModelTest: A free program written by David Posada that “estimates the model of DNA substitution that fits the data best among 56 models. MODELTEST calculates AIC values, AIC differences, Akaike weights and hierarchical likelihood ratio tests.”
Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
PAUP* 4.0: A program developed by David Swofford. Perhaps the most widely used phylogenetics software available. Distance, Parsimony, and Likelihood optimality criteria can be employed. It is distributed by Sinauer Press.
Swofford, D. L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and OtherMethods). Sinauer Associates, Sunderland, MA.
MacClade: “MacClade is a computer program for phylogenetic analysis written by David Maddison and Wayne Maddison. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.” It is distributed by Sinauer Press.
Maddison, W. P., and D. R. Maddison. 1992. MacClade: Analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, Massachusetts.
r8s:This is a free program written by Mike Sanderson. It is used to calculate divergence times in a phylogeny, even when the molecular data is not evolving in a clock-like fashion. The program provides the ability to calculate 95% confidence intervals surrounding estimated ages of nodes.
Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218-1231.
Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Molecular Biology and Evolution 19:101-109.
Sanderson, M. J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
COLLAPSE: A free program written by David Posada that is a tool for collapsing sequences to haplotypes. Current version is 1.2.
Arlequin: A free program written by Schneider et al (2000) which is probably one of the most widely used software packages for doing population genetic analyses, especially Analysis of Molecular Variance (AMOVA), genetic diversity measures, and Fst estimates. Also includes a program for constructing minimum spanning trees.
Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin ver. 2.000: A software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
Migrate: Migrate is a free program written by Beerli and Felsenstein (1999, 2001) that is part of Lamarc,a system for doing Likelihood Analysis with Metropolis Algorithm using Random Coalescence. Migrate estimates effective population sizes and past migration rates between two or n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes.
Beerli, P., and J. Felsenstein. 1999. Maximum likelihood estimation of a migration matrix and effective population numbers in two populations using a coalescent approach. Genetics 152:763-773.
Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Science, USA 98:4563-4568.
STRand: This free software has a similar function as ABI's GeneScan software - it allows a user to track a gel and to analyze and score microsatellite fragments. STRand allows you to run and analyze up to 96 lanes on an ABI-377 and offers a convenient way to organize and archive your data within the program.
MICROCHECKER: This free software identifies possible null alleles, large allele dropout, scoring errors due to stutter peaks, and possible typographic errors.
Van Oosterhout C, Hutchinson WF, Wills DPM, and Shipley P (2004) MICRO-CHECKER: software for identifying and correcting and genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535-538.
GENETIX 4.05: This free program converts genotypic data into formats used by many common genetic analysis software programs (e.g. Arlequin, Biosys, FSTAT, Genepop). The input format is simple and can be cut and pasted directly from an Excel spreadsheet. Populations can then be identified before exporting the data in an alternate format.
Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F. 1996-2004 GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France).