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Alaska Department of Fish and Game


Gene Conservation Laboratory
Statistics Program for Analyzing Mixtures (SPAM) Software

Our Mission

The mission of the Gene Conservation Laboratory is to apply genetic principles and tools to support the management of commercially important fish and shellfish species in Alaska based on the sustained yield principle.

Highlights

SPAM Genetic Data Analysis Links

SPAM software logo

Genetic Stock Identification

  • WhichRun2 - Windows 95 / 98 / NT Software for assigning individuals to populations based on multilocus genotype data. Created by Michael Banks (Hatfield Marine Science Center, Oregon State University)and Will Eichert (Bodega Marine Laboratory, University of California at Davis). THIS PACKAGE CAN CONVERT GENEPOP FILES TO SPAM INPUT FILES.
  • Assignment Calculator - from the work of Paetkau and co-authors. Java-script can be run over the web.
  • WhichLoci - computer program that selects the best combination of loci for population assignment through empiric analysis of data drawn from natural populations. This package allows selection of loci for genetic stock identification analysis. Created by Michael A. Banks, Will Eicher (Bodega Marine Laboratory) and J.B. Olsen (US FWS).
  • GMA - Genetic Mixture Analysis software. Similarly to SPAM it performs genetic stock identification (stock proportions and individual assignment) of mixture samples.

Population Genetic

  • Arlequin - Windows software offering extensive population genetics analyses, developed by the Laboratoire de Génétique & Biométrie in the Departement of Anthropology and Ecology at the University of Geneva, Switzerland. The laboratory also provides a number of other programs for haplotype frequency estimation in the face of missing data, AMOVA - analysis of molecular variance, etc.
  • Bottleneck - a program to detect recent effective population size reductions using allele frequency data. Developed at the Laboratoire de modélisation et biologie évolutive, Institut National de la Recherche Agronomique, Montpellier, France.
  • GDA: Software for analyzing discrete genetic data - Windows software designed to accompany Bruce Weir's "Genetic Data Analysis, 2ed".
  • GeneClass2 - Performs three major tasks on any microsatellite dataset harboring null alleles: (1) estimates null allele frequencies for each locus and population (2) estimates unbiased FST (3) computes a genotype dataset corrected for null alleles.
  • GenePop - Exact population genetics tests (H-W equilibrium, population differentiation, genotypic disequilibrium), population parameter estimation, etc. Created by Michel Raymond and François Rousset of the "Genetics of adaptation" Lab, Genetics and Environment, Institut des Sciences de l'Evolution Université de Montpellier, France.
  • LAMARC - Likilihood Analysis with Metropolis Algorithm using Random Coalescence. A package of programs from Joe Felsenstein's Lab (Univ. of Washington) for estimating population parameters such as population size, growth rate, migration rates, etc. via maximum likelihood.
  • Mark Miller's Analytical Software Page -Windows software for various population genetic analyses (includes a program to automate preparation of input files for Laurent Excoffier's WINAMOVA).
  • RSTCALC - PC software for populations structure analyses using microsatellite data. Written by Simon Goodman of The University of Edinburgh. This site offers a number of other packages for detecting bottlenecks from sequence data, conducting hybrid zone analyses, parentage analysis, etc.
  • ADMIX 2.0 - Computes population admixture estimates from molecular data (based on Bertorelle & Excoffier 1998).
  • Structure - Software to investigate population structure using multilocus genotype data (microsatellites, RFLPs, etc.). Used in the article: J.K. Pritchard, M. Stephens and P. Donnelly, 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
  • SIMCOAL: general coalescent program for simulating molecular data in interconnected populations with arbitrary demography. Excoffier, Novembre, and Schneider.
  • MICSAT - MCMC sampling of coalescent trees for microsatellite loci. Wilson & Balding.
  • Quantitative Genetics Analysis Programs - part of Dr. Patrick Phillips website at Ecology and Evolution, University of Oregon.

Evolutionary Genetics

  • Joe Felsenstein's Lab - Dept. of Genetics, University of Washington. Home of the PHYLIP phylogeny inference package, a large list of other phylogeny programs, the LAMARC coalescent likelihood package, etc.

History / Educational Sites

  • Enter Evolution: Theory and History - The UC Berkeley Museum of Paleontology's online exhibits on evolution. Includes historical time line of key players in the development of evolutionary theory, an introduction to systematics and cladistics, and much more. Be sure to visit the other online exhibits.
  • MendelWeb - Built around Mendel's 1865 paper (translated as "Experiments in Plant Hybridization"), MendelWeb is a hypertext introduction and exploration of "the origins of classical genetics, data analysis, elementary plant science, and the history of science." See, especially, the Essays and Commentary section.
  • The Virtual Library: Biosciences - Just what the name implies. From Biodiversity and Ecology to Zoology - a compendium of articles, links, information,etc.

Other Genetics Lists

  • Genetic Analysis Software - Computer software on the following topics: genetic linkage analysis, marker mapping, linkage disequilibrium mapping, and pedigree drawing. Created by Dr. Wentian Li, North Shore LIJ Research Institute.
  • The Biocatalog - European Bioinformatics Institute software directory of general interest in genetics and molecular biology.
  • Genetics Journal

Links to Other Genetics Sites