Genetic Data Analysis

Below are a number of programs focusing on the analysis/generation of genetic data. The focus is on MLE (maximum likelihood) or bayesian estimation of parameters of interest. However, you will notice that not all programs have this focus - some are included because they are helpful/widely used. Although I have tried most of these programs, I cannot ensure that all will work as promised with your results.

PDF references and link information are provided. PDF downloads are limited to those within my research group (@ UGA).

Categories

Reviews of Analysis Programs

  1. PDF | Excoffier, Heckel. 2006. Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics 7, 745-758.

Data Conversion

  1. PDF | Glaubitz, J. 2004. CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4:309-310.

  2. PDF | Faircloth, B. 2006. GMCONVERT: file conversion for GENEMAPPER output files. Molecular Ecology Notes 6:968-970.

  3. [PDF] | Manoukis, N. 2006. Formatomatic: Population Genetic File Creator and Converter. Available from author.

General Analysis Programs

  1. PDF | Raymond M., Rousset F, 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249

  2. PDF | Peakall R., Smouse P. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6:288–295

Statistical Correction

  1. PDF | Rice. 1989. Analyzing tables of statistical data. Evolution. 43:223-225.
  2. PDF | Narum. 2006. Beyond Bonferroni: Less conservative analyses for conservation genetics. Conservation Genetics. 7:783-787.

Population Substructure

  1. PDF | Pritchard J, Stephens M, Donnelly P. 2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics 155:945-959.

  2. PDF | Holsinger. 1999. Analysis of Genetic Diversity in Geographically Structured Populations: A Bayesian Perspective. Hereditas. 130:245-255.

  3. PDF | Corander J, Waldmann P, Sillanpaa MJ. 2003. Bayesian analysis of genetic differentiation between populations. Genetics 163: 367–374.

  4. PDF | Corander J, Waldmann P, Marttinen P, Sillanpaa MJ. 2004. BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20: 2363–2369.

  5. PDF | Baolin Wu, Nianjun Liu, and Hongyu Zhao. 2006. PSMIX: an R package for population structure inference via maximum likelihood method. BMC Bioinformatics 7:317.

Spatial Genetic Data Analysis

  1. PDF | Hardy, O., Vekemans, X. 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2:618–620.

  2. PDF | Guillot, G., Mortier, F., Estoup, A. 2005. GENELAND: a computer package for landscape genetics. Molecular Ecology Notes 5:712-715.

Parentage Analysis

  1. PDF | Hadfield, J. D., Richardson, D. S., Burke, T. 2006. Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology (online early).

  2. PDF | Jones, A. 2005. GERUD 2.0: a computer program for the reconstruction of parental genotypes from half-sib progeny arrays with known or unknown parents. Molecular Ecology Notes 5:708-711

  3. PDF | Marshall T.C., Slate J., Kruuk L.E.B., Pemberton J.M. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639-655.

  4. PDF | Slate J., Marshall T.C., Pemberton J.M. 2000. A retrospective assessment of the accuracy of the paternity inference program CERVUS. Molecular Ecology 9: 801-808.

  5. [PDF] | Kalinowski, S.T., Taper, M.L., Marshall, T.C. 2006. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology. In press.

  6. PDF | Taggart, J.B. 2006. FAP: an exclusion-based parental assignment program with enhanced predictive functions. Molecular Ecology Notes. In press.

Relatedness

  1. PDF | Kalinowski S.T., Wagner, A.P., Taper, M.L. 2006. ML-RELATE: a computer program for maximum likelihood estimation of relatedness and relationship. Molecular Ecology Notes 6:576–579.

  2. PDF | Queller D.C., Goodnight K. F. 1989. Estimating relatedness using genetic markers. Evolution 43:258-275.

Tree Generation

  1. PDF | Huelsenbeck, J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.

  2. PDF | Ronquist, F., Huelsenbeck, J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.

  3. PDF | Posada D., Crandall K.A., Templeton A.R. 2006. Nested clade analysis statistics. Molecular Ecology Notes 6:590-593.

Genetic Data Simulation

  1. Foward-time simulation programs:

    1. PDF | Guillaume, F., Rougemont, J. 2006. Nemo: an evolutionary and population genetics programming framework. Bioinformatics 22:2556-2557

    2. PDF | Peng, B., Kimmel, M. 2005. simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21: 3686–3687.

      • Link | simuPop (WIN, OSX, LINUX)

  2. Reverse-time (Coalescent) programs:

    1. PDF | T. Mailund, Schierup M.H. , Pedersen C.N.S., Mechlenborg P.J.M., Madsen J.N., Schauser, L. 2005. CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models. BMC Bioinformatics 6:252.

  3. Other:

    1. PDF | Balloux, F. 2001. EASYPOP (version 1.7): A computer program for the simulation of population genetics. J. Heredity 92: 301-302.

    2. HTML | Olivier T. 2006. Documentation for the Crittrz Population Simulation Kit, Version 0.7.5

    3. PDF | Anderson, E.C., Dunham, K.K. 2005. spip 1.0: a program for simulating pedigrees and genetic data in age-structured populations. Molecular Ecology Notes 5:459-461.

    4. PDF | Pidugu S., and Schlotterer, C. 2006. ms2ms.pl: a PERL script for generating microsatellite data. Molecular Ecology Notes 6:580-581.

Modified: 02/12/2007 12:31