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| L'ABAT
L’Action Boréale in Abitibi-Témiscamingue (president:
Richard Desjardins).http://www.actionboreale.qc.ca/ |
Canada’s Aquatic Environments
Information on research, conservation and aquatic biodiversity in Canada.http://www.aquatic.uoguelph.ca/ |
Canadian Rivers Institute
Applied research focusing on rivers ecosystems.http://www.unb.ca/cri |
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COSEWIC
Committee on the status of endangered wildlife in Canada.http://www.cosewic.gc.ca/index.htm |
CWS
Environment Canada.http://www.ec.gc.ca/ |
EAU SECOURS
Québécois Coalition for responsible management of water resources.http://www.eausecours.org/ |
| FONDATION DE LA FAUNE DU
QUÉBEC
Non-profit organisation dedicated to the protection of biodiversiy in Quebec.http://www.fondationdelafaune.qc.ca/ |
| GREMM
The Group for research and eduction on marine mammals.http://www.gremm.org/ |
MRNFP
Richesses Naturelles et Faune Québec.http://www.mrnfp.gouv.qc.ca/ |
RESCOUSSE
A beer for threatened species.http://www.rescousse.qc.ca/ |
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| Convention on International Trade in Endangered Species of Wild Fauna and Flora
http://www.cites.org/ |
ESA
Endangered Species Act (USA).http://endangered.fws.gov/esa.html |
| FAO
Food and Agriculture Organization of the United Nations.http://www.fao.org/ |
FISHBASE
Site dedicated to the world fish biodiversity (28 100 fish species, 35 300 photos).http://www.fishbase.org/search.html |
| MONTERY BAY AQUARIUM, Seafood
watch
For chosing the right seafood and fish to eat.http://www.mbayaq.org/ |
IUCN - The World Conservation Union
Organization that promotes the protection of biodiversity and an equitable use of natural resources.http://www.iucn.org/ |
| UNEP-WCMC Species Database
Threatened species of the world.http://www.unep-wcmc.org |
U.S. Fish and Wildlife Service (Endangered species list)
http://endangered.fws.gov/ |
| World Resources Institute
http://www.wri.org/ |
WWF
Fonds Mondial pour la Nature.http://www.wwf.ca/ |
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Céline
Audet
ISMER, l’Institut des Sciences de la Mer de Rimouski.Université du Québec à Rimouski, Québec, Canada http://www.pqm.net/ismer/index.html |
Dave J. Basley (david.basley@state.me.us)
Maine Department of Inland Fisheries and Wildlife
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Luciano Beheregaray
Dept. of Biological Sciences, Macquarie UniversitySydney, Australia http://www.bio.mq.edu.au/molecularecology/ |
Pierre Belhumeur
Université de Montréal, Québec, Canadahttp://www.microim.umontreal.ca/asp/Bottin/BottinPlus.asp?ID=50 |
| Jasminca Behrmann-Godel Universität Konstanz Limnologisches Institut http://www.uni-konstanz.de/fish-ecology/behrmann_godel.htm |
Pierre Blier
Université du Québec à Rimouski, Québec, Canada http://www.uqar.qc.ca/bcss/bio/Personnel/PBlier1.htm |
Edwin Bourget
Université de Sherbrooke, Québec Canada &Québec-Océan, Le Groupe interinstitutionnel de recherches océanographiques du Québec Université Laval, Québec, Canada http://www.usherbrooke.ca/ |
Peter Campbell
INRS, Eau, terre et environnementhttp://www.ete.inrs.ca/peter-gc-campbell |
François Caron (Francois.Caron@fapaq.gouv.qc.ca)
Ressources naturelles et Faune Québec (MRNF), Québechttp://www.fapaq.gouv.qc.ca/ |
| Martin Castonguay Institut Maurice Lamontagne Pêches et Océans Canada http://www.qc.dfo-mpo.gc.ca/iml/fr/intro.htm Martin.Castonguay@dfo-mpo.gc.ca |
| Maria Manuela Coelho Faculdade de Ciências da Universidade de Lisboa. Departamento de Biologia Animal http://ffishgul.fc.ul.pt |
Steeve Côté
Département de biologieUniversité Laval, Québec, Canada http://www.bio.ulaval.ca/en/accueil.aspx?tabid=166 Centre d’Études Nordiques (CEN) Université Laval, Québec, Canada http://www.cen.ulaval.ca |
Patrice Couture
INRS Eau, Terre & Environnementhttp://www.ete.inrs.ca/patrice-couture |
Daniel Cyr
INRS-Institut Armand Frappier.http://www.iaf.inrs.ca/daniel-g-cyr |
Roy Danzmann
University of Guelph, ON, Canadahttp://www.uoguelph.ca/~rdanzman/ |
| Nicolas Derome Département de biologie, Université Laval http://www.bio.ulaval.ca/no_cache/departement/professeurs/fiche_des_professeurs/professeur/11/240/ |
| Mélanie Dionne Biologist, Ministère des Ressources Naturelles et de la Faune, Québec, Qc melanie.dionne@mrnf.gouv.qc.ca |
Julian Dodson
Département de biologieUniversité Laval, Québec, Canada http://www.bio.ulaval.ca/en/accueil.aspx?tabid=167 CIRSA, Centre Interuniversitaire de Recherche sur le Saumon Atlantique Université Laval, Québec, Canada http://www.bio.ulaval.ca/cirsa/ |
Pierre Dumont (pierre.dumont@fapaq.gouv.qc.ca)
Ressources naturelles et Faune Québec (MRNF), Québechttp://www.fapaq.gouv.qc.ca/ |
Sigurd Einum
NINA Norwegian Institute for Nature Research, Norwayhttp://www.nina.no |
Dany Garant
Département de biologie, Université de Sherbrooke.http://www.usherbrooke.ca/biologie/personnel/professeurs/ecologie-terrestre/dany-garant/ |
Gilles Gauthier
Département de biologieUniversité Laval, Québec, Canada http://www.bio.ulaval.ca/en/accueil.aspx?tabid=170 Centre d’Études Nordiques (CEN) Université Laval, Québec, Canada http://www.cen.ulaval.ca |
Helga Guderley
Département de biologieUniversité Laval, Québec, Canada http://www.bio.ulaval.ca/accueil.aspx?tabid=171 Québec-Océan, Le Groupe interinstitutionnel de recherches océanographiques du Québec Université Laval, Québec, Canada http://www.quebec-ocean.ulaval.ca/ |
| Robert Hanner Biodiversity Institute of Ontario & Department of Intergrative Biology, University of Guelph http://www.uoguelph.ca/~phebert/ |
Michael Hansen
Dannish Institute of Fisheries Research, Denmarkhttp://www.aqua.dtu.dk/English.aspx |
Paul Hebert
Department of Intergrative Biology, University of Guelph, Guelph.http://www.uoguelph.ca/~phebert/ |
Kjetil Hindar
NINA Norwegian Institute for Nature Research, Norwayhttp://www.nina.no |
Jeffrey Hutchings
Department of Biology, Dalhousie university.http://biology.dal.ca/People/faculty/hutchings/hutchings.htm |
Bjarni Jónsson
Institute of Freshwater FisheriesHolar, Iceland http://www.veidimal.is/ |
Tim King (tlking@usgs.gov)
Leetown Science Center, USGShttp://www.lsc.usgs.gov/ |
Roger Lévesque |
Richard Mayden
Biology DepartementSaint-Louis University, MO, US http://bio.slu.edu/mayden/home.html |
| Pierre Magnan Département de chimie-biologie, Université du Québec à Trois-Rivières http://www2.uqtr.ca/GREA/chercheurs.php?id=5 |
Yves Mailhot (yves.mailhot@fapaq.gouv.qc.ca)
Ressources naturelles et Faune Québec (MRNF), Québechttp://www.fapaq.gouv.qc.ca/ |
Kristina Miller
Department of Fisheries and OceansPacific Biological Station, Nanaimo, B.C. Canada http://www.pac.dfo-mpo.gc.ca/sci/pbs/ |
| Marc Mingelbier Ressources Naturelles et Faune Québec, Service de la Faune Aquatique http://www.mrnf.gouv.qc.ca/ marc.mingelbier@mrnf.gouv.qc.ca |
Tor Naesje
NINA Norwegian Institute for Nature Research, Norwayhttp://www.nina.no |
| Michel Plante Parc National de la Mauricie http://www.pc.gc.ca/pn-np/qc/mauricie/index_F.asp michel.plante@pc.gc.ca |
Ciro Rico
Estacion Biologia de Donana, Sevilla, Espanahttp://www.ebd.csic.es/ |
François Shaffer (francois.shaffer@ec.gc.ca)
ISCF, Service Canadien de la FauneQuébec, Canada http://www.ec.gc.ca/ |
Daniel Toussaint (Daniel.toussaint@fapaq.gouv.qc.ca)
Ressources naturelles et Faune Québec (MRNF), Québechttp://www.fapaq.gouv.qc.ca/ |
George Turner
Molecular Ecology and Fisheries Genetics LaboratoryUniverity of Hull, U.K. http://www.hull.ac.uk/biosci/staff/academic/MolecularEcologyandEvolution/GeorgeTurner.html |
Warwick Vincent
Département de biologieUniversité Laval, Québec, Canada http://www.bio.ulaval.ca/accueil.aspx?tabid=183 Centre d’Études Nordiques (CEN) Université Laval, Québec, Canada http://www.cen.ulaval.ca |
Asbjørn Vøllestad
Department of BiologyUniversity of Oslo http://www.bio.uio.no/akv/english/staff/biography/vollestad_Asbjorn.html |
Graham Wallis
Department of ZoologyUniversity of Otago, Dunedin, New Zealand http://www.otago.ac.nz/Zoology/staff/otago008937.html |
Henri Weimerskirch
CNRS, Centre d’Études Biologiques de Chizé, Francehttp://www.cebc.cnrs.fr/ |
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Fred Allendorf
University of Montana, U.S.A.(Bibliography with more than 50 000 references) http://dbs.umt.edu/people/facultyDetails.php?id=873 |
| Bernard Angers Département des Sciences Biologiques, Université de Montréal http://www.bio.umontreal.ca/personnel/ANGERS_Bernard/index.html |
Paul Bentzen
DFO Chair, Fisheries Resource ConservationDalhousie University, N.S. Canada http://biology.dal.ca/People/faculty/bentzen/bentzen.htm |
Giacomo Bernardi
Molecular Ecology and Evolution of FishesUniversity of California, Santa Cruz, U.S.A. http://bio.research.ucsc.edu/people/bernardi/ |
| Michael Blouin Deaprtment of Zoology, Oregon State University http://oregonstate.edu/~blouinm/index.htm |
François Bonhomme
Génome, Populations Interactions AdaptationUniversité de Montpellier, France http://www.univ-montp2.fr/%7Egenetix/index.htm#thema |
Brian Bowen
Hawaii Institute of Marine Biology, U.S.A.http://www.hawaii.edu/HIMB/ |
Gary Carvalho
Molecular Ecology and Fisheries Genetics LaboratoryUniverity of Hull, U.K. http://www.hull.ac.uk/molecol/index.html |
Robert W. Chapman
South Carolina Department of Natural Resourceswww.marinegenomics.org |
Dan Heath
Great Lakes Institute for the Environment University of Winsdor, ON, Canada http://cronus.uwindsor.ca/units/glier/NewMain.nsf/inToc/560038DDEA988E2185256E5900527CC3 |
Andrew Hendry
Redpath MuseumMcGill University, Québec, Canada http://ww2.mcgill.ca/biology/faculty/hendry/ |
Bill Jordan
Senior Research FellowInstitute of Zoology, London, UK. http://www.zoo.cam.ac.uk/ioz/index.htm |
David Kingsley
Genome Evolution CenterStanford University, U.S.A. http://cegs.stanford.edu/index.jsp |
Michael Kinnison
University of Maine, U.S.A.http://biology.umaine.edu/ |
Tom Kocher
Hubbard Center for Genome StudiesUniversity of New Hampshire, U.S.A. http://hcgs.unh.edu/ |
Ben Koop
GRASP (Genomic Research on Atlantic Salmon Project)University of Victoria, B.C., Canada http://web.uvic.ca/cbr/grasp/ |
Axel Meyer
University of Konstanz, Germanyhttp://www.evolutionsbiologie.uni-konstanz.de/ |
Dr. Brian Neff
Department of BiologyUniversity of Western Ontario, ON, Canada http://www.uwo.ca/biology/Faculty/neff/index.htm |
Craig Primmer
Department of Biology at the University of Turku, Finlandhttp://users.utu.fi/primmer/ |
| Beren Robinson Deaprtment of Integrative Biology, University of Guelph http://www.uoguelph.ca/ib/faculty/faculty_robinson.shtml |
Daniel Ruzzante
Canadian Research Chair in Marine Conservation GeneticsDalhousie University, N.S., Canada http://biology.dal.ca/us/f/ruzzante/ruzzante.htm |
Dolph Schluter
University of British Columbia, B.C., Canadahttp://www.zoology.ubc.ca/~schluter/ |
Kim Scribner
Molecular Ecology LaboratoryMichigan State University, U.S.A. http://www.fw.msu.edu/people/ScribnerKim/ |
Eric Taylor
UBC Center for Biodiversity ResearchUniversity of British Columbia, B.C., Canada http://www.zoology.ubc.ca/~etaylor/index.html |
Filip Volckaert
Lab. Aquatische ecologie, Leuven, Belgiumhttp://cwisdb.cc.kuleuven.be/persdb-bin/persdb |
Robin Waples
Northwest Fisheries Science Center, U.S.Ahttp://www.nwfsc.noaa.gov/ |
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CERVUS
Kalinowski, ST, Taper, ML & Marshall, TC (2007) Molecular Ecology 16: 1099-1006.Computer program for parentage analyses (assignment of parents to their offspring) using co-dominant loci. Simulations can be used to determine the power of the analyses. http://www.fieldgenetics.com/pages/aboutCervus_Overview.jsp |
COLONY
WANG J (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963-1979.Maximum likelihood method that assigns individuals in a sample into full-sib families nested within half-sib families (colonies) using data on co-dominant genetic markers. http://www.zoo.cam.ac.uk/ioz/software.htm#COLONY |
DELRIOUS
Stone J and Bjorkland M (2002) Molecular Ecology Notes.Relatedness (r) estimates based on Lynch and Ritland K (1999) Mathematica. http://www.zoo.utoronto.ca/stone/DELRIOUS/delrious.htm |
IDENTIX
Bonhomme F, Castric V and Bernatchez L (2002) Molecular Ecology Notes.A program to test relatedness in a population using permutation methods. http://gepv.univ-lille1.fr/english/perso_pages_en/PagepersoVincent_c.htm |
KINGROUP
KONOVALOV DA, MANNING C and HENSHAW MT (2004) KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers Molecular Ecology Notes 4:779-782.Open source java program implementing a maximum likelihood approach to pedigree relationships reconstruction and kin group assignment.. http://www.it.jcu.edu.au/kingroup |
KINSHIP
Goodnight’s software for population biology. Performs maximum likelihood tests of pedigree relationships between pairs of individuals in a population. The calculation includes a simulation procedure to determine the statistical significance of results.http://www.gsoftnet.us/GSoft.html |
MER
Wang J (2002) Genetics 160:1203-1215.Estimate the relatedness coefficients between individuals from codominant genetic markers. Bootstrapping over loci is used to estimate standard deviations of the estimates. http://www.zoo.cam.ac.uk/ioz/software.htm/ |
PAPA
Duchesne P, Godbout M-H, L Bernatchez L (2002) Molecular Ecology Notes 2:191-194.A computer program for simulated and real parental allocation. Include a simulator for estimating assignment success under various scenarios. http://www.bio.ulaval.ca/louisbernatchez/downloads.htm |
PARENTÉ
Cercueil A, Bellemain E and Manel S (2002) Journal of Heredity 93: 458-459.Computer program for parentage analysis. http://www-leca.ujf-grenoble.fr/logiciels.htm |
PASOS
Duchesne P, Castric T and L Bernatchez (2005) Molecular Ecology Notes 5:701-704.Parental allocation and simulator program to be used in open systems i.e. when some proportion of the true parents have not been collected/genotyped. designed to assess parentage, detect the proportion of uncollected parents, and calculate estimates of the probability that allocations are correct through simulations. http://www.bio.ulaval.ca/louisbernatchez/downloads.htm |
PEDIGREE
Herbinger C (2005).Set of algorithms and routines to reconstruct full pedigree in a group of individuals based on their genotype data, and this in the complete absence of parental information. Possibilities to potentially reconstruct the set of single generation relationships among individuals i.e. which individuals are most likely full-sibs, half-sibs and unrelated. In addition, it allows generating the genotype of the unknown parents and testing the significance of the pedigree obtained. http://herbinger.biology.dal.ca:5080/Pedigree/ |
RELATEDNESS
Goodnight’s software for population biology.Estimate average relatedness between pairs of individuals or within groups. http://www.gsoftnet.us/GSoft.html |
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ADMIX
Dupanloup I, and Bertorelle G (2001) Molecular Biology and Evolution 18: 672-675.Computes admixture proportions for a given population or group of individuals to any number of parental populations using either allele frequencies or accounting for molecular divergence between alleles. http://cmpg.unibe.ch/software/admix/ |
AFLPOP
Duchesne P and Bernatchez L (2002) Molecular Ecology Notes 3:380-383.A computer program for simulated and real population allocation based on AFLP data. Includes a simulator allowing to test the probability of genotypes to be F1, F2 or BC hybrids. http://www.bio.ulaval.ca/louisbernatchez/downloads.htm |
BAPS
Coriander J, Waldmann P and Sillanpää MJ (2003) Genetics 163:367-374Bayesian assessment to determine the number of genetically distinct populations. Treats populations as units, uses prior information about the sampling locations. http://www.rni.helsinki.fi/~jic/bapspage.html |
BAYESASS
Wilson GA and Rannalaa B (2003) Genetics 163:1177-1191.Estimation of recent migration rates (m) between populations. http://www.rannala.org/labpages/software.html |
BAYES STOCK ADMIXTURE METHODS
Pella JM and Matsuda M (2001) Fishery Bulletin 99:151-167.Bayesian estimation of stock composition for mixed stock analysis. http://fishbull.noaa.gov/991/13.pdf |
DISTRUCT
Rosenberg NA (2004) Molecular Ecology Notes 4:137-138Enables graphical display of Structure output and allows for additional optional files. http://rosenberglab.bioinformatics.med.umich.edu/software.html |
Family-Sim
Program written in C that will take an allele frequency file and use those data to generate a user-defined number of individuals of known relatedness.http://web.me.com/tfrasier/Frasier_Lab/Software.html |
GENECLASS
Cornuet J-M, Piry S, Luikart G, Estoup A and Solignac M (1999) Genetics 153:1989-2000.Bayesian, frequency and exclusion methods of assignment tests. http://www.montpellier.inra.fr/URLB/ |
HYBRIDLAB
Nielsen EE, Hansen MM and Bach LA (2001) Conservation genetics 2:219-232.Simulation of hybrid individuals based on multilocus genotypic data. http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1471-8286.2006.01433.x |
IMMANC
Rannala B and Mountain JL (1997) PNAS 94: 9197-9201. Detects immigrants using multilocus genotypes. http://www.rannala.org/labpages/software.html |
LEA
Chikhi L, Bruford MW and Beaumont MA (2001). Genetics 158:1347-1362.Program for estimating admixture proportions. http://www.rubic.rdg.ac.uk/%7Emab/software.html |
NEWHYBRIDS
Anderson EC and ThompsonEA (2002) Genetics 160:1217-1229.Provides posterior distribution that individuals fall into different hybrid categories betwen 2 populations–dominant or co-dominant markers. http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm |
PARTITION
Belkhir K and KJ Dawson KJ (2001) Genetical Research 78:59-77.Statistical software package for identifying population sub-division and assigning individuals to populations. http://www.univ-montp2.fr/%7Egenetix/#programmes |
SPAM
Devebec EM, Gates RB, Masuda M, Pella J, Reynolds J and Seeb LW (2000) Journal of Heredity 91:509 - 510.A program that estimates the relative contributions of discrete populations to a mixture sample. http://www.cf.adfg.state.ak.us/geninfo/research/genetics/software/spampage.php |
STRUCTURE
Pritchard JK, Stephens M and Donnelly P (2000) Genetics 155:945-959.Individual admixture, population assignment, population clustering (k). http://pritch.bsd.uchicago.edu/software.html |
STRUCASSIGN
Manel S, Luikart G and Cornuet J-M (2002) Conservation Biology 16:650-659.Modifies STRUCTURE assignment to give leave-one-out-method for comparisons with GENECLASS. *** Available from the authors at request *** |
WHICHRUN
Banks MA and Eichert W (2000) Journal of Heredity 91:87-89.A computer program for population assignment of individuals based on multilocus genotype data. http://www-bml.ucdavis.edu/whichrun.htm |
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AFLP-SURV
Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Molecular Ecology 11:139-151 Estimates genetic diversity and population genetic structure from population samples analysed with AFLP or RAPD methods and computes genetic distance matrices between populations. http://www.ulb.ac.be/sciences/lagev/aflp-surv.html |
ARLEQUIN
Schneider S, Roessli D and Excoffier L (2000) University of Geneva, SwitzerlandSoftware for population genetics data analysis, including genetic differentiation and analyses of molecular variance (AMOVA). http://lgb.unige.ch/arlequin/ |
BARRIERS 2.2
Manni F, Guérard E and Heyer E (2004) Human Biology 76:173-190Computes geographic barriers from a distance matrix. Uses a monmonnier algorithm to detect barriers in genetic, morphological, and linguistic data. http://www.mnhn.fr/mnhn/ecoanthropologie/software/barrier.html |
BOTTLENECK
Cornuet J-M et Luikart G (1997) Genetics 144:2001-2014. A program for detecting recent effective population size reductions from allele data frequencies. http://www.montpellier.inra.fr/URLB/ |
COLONISE 1.0
Gaggiotti OE, Brooks SP, Amos W and Harwood J (2004) Molecular Ecology 13: 811-825Software for the study of colonisation events in natural populations. It determines the composition of the newly colonised population and makes inferences about the factors that influenced individuals to establish a new population. http://www-leca.ujf-grenoble.fr/logiciels.htm |
CONVERT
Glaubitz JC (2004) Molecular Ecology Notes 4:309-310A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. http://www.agriculture.purdue.edu/fnr/html/faculty/Rhodes/Students%20and%20Staff/glaubitz/software.htm |
DIVAGE
Bertorelle G and Rannala B (in Press) PNAS.MLE of population divergence times between two populations. http://web.unife.it/progetti/genetica/Giorgio/giorgio_soft.html |
DnaSP
Rozas J and Rozas R () Bioinformatics 15: 174-75.A program for analysis of nucleotide polymorphism from aligned DNA sequence data, neutrality tests. It estimates the confidence intervals of some test-statistics by the coalescent. http://www.ub.es/dnasp/ |
EASYPOP
Balloux F, Brünner H, Lugon-Moulin N, Hausser J and Goudet J (2000) Evolution 54:1414-1422A simulation software for population genetics. http://www.unil.ch/dee/page6759.html |
FORMATOMATIC
Manoukis NC (2007) Molecular Ecology Notes 7:592-593.A program for converting diploid allelic data between common formats for population genetic analysis. http://taylor0.biology.ucla.edu/manoukis/Pub_programs/Formatomatic/ |
FSTAT
Goudet J (1995). Journal of Heredity 86: 485-486.A program for estimating and testing gene diversities and differentiation statistics from codominant genetic markers. http://www.unil.ch/dee/page6759_en.html |
GDA- Genetic Data Analysis
v4.05
Software for the analysis of population structure data. Basic population
genetic parameters, F-statistics and test for disequilibrium.http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php |
GENALEX 6
Peakall R, and Smouse P.E. (2006) Molecular Ecology Notes 6: 288–295.Cross-platform package for population genetic analysis that runs within Microsoft Excel. http://www.anu.edu.au/BoZo/GenAlEx/ |
GENELAND
Geneland computes landscape genetic analyses. It uses geographic coordinates
of individuals and multilocus genetic data to estimate the number of
populations in a dataset and delineate their spatial organisation. Works
within the R package.http://www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/Geneland.html |
GENETIX
Belkhir K, Borsa P, Chikhi L, Raufaste N and Bonhomme F (1996-2002) GENETIX 4.04, software under Windows for population genetics. A program for population genetics data analysis, including genetic differentiation, standard statistics (e.g. heterozygosity, allele frequencies) Factorial Component analysis (FCA). http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm |
GENEPOP
Raymond M and Rousset F (1995) Journal of Heredity 86:248-249.Population genetics software for exact tests and ecumenicism. http://genepop.curtin.edu.au/ |
GENGIS
Beiko, R., Whalley, J., Wang, S., Clair, H., Smolyn, G., Churcher, S., Porter, M., Blouin, C., & Brooks, S. (2008).Application that allows users to combine digital map data with information about biological sequences collected from the environment. http://kiwi.cs.dal.ca/GenGIS/Main_Page |
GEODIS
Posada D, Crandall KA and Templeton AR (2000) Molecular Ecology 9:487-488.Software for nested-clade analysis (NCA). http://darwin.uvigo.es/software/geodis.html |
GESTE
Foll, M and Gaggiotti O (2006) Genetics 174: 875-891.GEnetic STructure inference based on genetic and Environmental data is a Bayesian method to evaluate the effect that biotic and abiotic environmental factors have on the genetic structure of populations. http://www-leca.ujf-grenoble.fr/logiciels.htm |
IR_MACRO
Bill Amos University of Cambridge.This macro calculates a number of different measures of heterozygosity for use in the analysis of heterozygosity-fitness calculations. http://www.zoo.cam.ac.uk/zoostaff/amos/ |
MCLEEPS
Anderson EC et Thompson EA (2000) GENETICS 156:2109-2118. A temporal method for estimating Ne using a maximum likelihood based approach. http://www.stat.washington.edu/thompson/Genepi/Mcleeps.shtml |
MDIV
Nielsen R Wakeley J (2001) Genetics 158:885-896.Coalescent method to jointly estimates migration rates, time of divergence, and historical effective population size (Ne) using sequence data. http://www.binf.ku.dk/~rasmus/webpage/programs.html |
MicroM_test and Critical_M
Garza J, Williamson E (2001) Molecular Ecology, 10: 305–318.The ratio of the number of alleles to range in allele size, for a sample of microsatellite loci can be used to detect reductions in effective population size. http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3298 |
Microsatellite analyzer (MSA)
Dieringer D et Schlötterer C (2003) Molecular Ecology Notes 3:167-169.Software tool designed to handle large microsatellite data sets. calculates the standard suit of descriptive statistics and provides input files for other software packages. http://i122server.vu-wien.ac.at/MSA/info.html/MSA_info.html |
MIGRATE
Beerli P and Felsenstein J (2001) PNAS 98:4563-4568. Coalescent-based method for estimating migration rates from a n population matrix and effective population size. http://evolution.genetics.washington.edu/lamarc/index.html |
MIGRLIB
Tufto J, Engen S and Hindar K (1996) Genetics 144:1911-1921.A program for inferring migration from gene frequencies. http://www.math.ntnu.no/~jarlet/migration |
MLNE
Wang J and Whitlock MC (2003) Genetics 163: 429-446.Joint maximum likelihood estimation of effective population size and migration rate. http://www.zoo.cam.ac.uk/ioz/software.htm |
MULTSIM
Noor MAF, M. Pascual M and Smith KR (2000) Evolution 54:696-703.Software for analysing the numbers of individuals that founded a population following a bottleneck or founder event. http://www.biology.duke.edu/noorlab/multsim.html |
MSVAR0.4.1B.ZIP
Beaumont M (1999) Genetics 153:2013-2029.A program for detecting past population growth or decline. http://www.rubic.rdg.ac.uk/%7emab/software.html |
NE ESTIMATOR
Molecular Fisheries Laboratory, Queensland, AustraliaMethods for estimating Ne from three different temporal methods. http://www2.dpi.qld.gov.au/fishweb/13887.html |
NEMO
Nemo is a forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of life history/phenotypic traits and population genetics in a flexible (meta-)population framework.http://nemo2.sourceforge.net/ |
NUCLEODIV
Holsinger KE and Mason-Gamer RJ (1996) Genetics 142:629-639.Hierarchical analysis of nucleotide diversity between populations. http://darwin.eeb.uconn.edu/#software |
PCAGEN
Goudet J (1999) Université de Lauzanne.Performs principal component analysis on gene frequency data. http://www.unil.ch/Jahia/site/dee/op/edit/pid/36924 |
POPGENE
Yeh F, Yang R and Boyle T (2001) University of AlbertaAnalysis of genetic variation among and within populations. http://www.ualberta.ca/~fyeh/index.htm |
RSTCALC
Goodman SJ (1997) Molecular Ecology 6:881-885. Estimation of Rst and assessment of its significance with bootstrapping. http://helios.bto.ed.ac.uk/evolgen |
SalmonNb
Waples R.S., Masuda M. and Pella J. (2007) Molecular Ecology Notes 7: 21-24.Estimate effective population size in salmon using temporal genetic data. ftp://ftp.afsc.noaa.gov/Sida/SalmonNb/ |
SAMOVA
Dupanloup I, Schneider S, Excoffier L (2002) Molecular Ecology 11:2571-81.Spatial analysis of molecular variance without a priori population designation. http://web.unife.it/progetti/genetica/Isabelle/samova.html |
SPAGEDI
Hardy OJ and Vekemans X (2002) Molecular Ecology Notes 2:618-620.A program for the spatial pattern analysis of genetic diversity. http://www.ulb.ac.be/sciences/ecoevol/spagedi.html |
Allele permutation test (in
SPAGEDI)
Hardy OJ, Charbonnel N, Fleville H and Heueurtz M (2003) Genetics 163: 1467-1482.Significance testing for Rst vs Fst (mutation vs. drift) for population differentiation. http://www.ulb.ac.be/sciences/ecoevol/spagedi.html |
TESS
François O., Ancelet S. and Guillot G. (2006) Genetics 174: 805-816.Bayesian clustering method using tessellations and MCMC in spatial population genetics. http://www-timc.imag.fr/Olivier.Francois/tess.html |
TFPGA
Mark Miller (1997) Utah State UniversityTools for population genetics analysis. http://bioweb.usu.edu/mpmbio/index.htm |
TM3
Berthier P, Beaumont MA, Cornuet J-M and Luikart G (2002) Genetics 160:741-751Maximum-likelihood estimation of effective population size (using temporal method). http://www.rubic.rdg.ac.uk/%7emab/software.html |
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ARCHAEOPTERYX
Java application for the visualization of annotated phylogenetic trees.http://www.phylosoft.org/archaeopteryx/ |
BEAST
Drummond AJ Nicholls GK Rodrigo AG and Solomon W (2002) Genetics 161:1307-1320. Bayesian MCMC analysis of molecular sequences, oriented towards molecular clock analyses. (OS X, Win, Java). http://evolve.zoo.ox.ac.uk/beast/ |
BIOEDIT
Hall TA (1999) Nucl. Acids. Symp. Ser. 41:95-98Sequence editor. http://www.mbio.ncsu.edu/BioEdit/bioedit.html |
CLUSTALX
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG (1997) Nucl. Acids Res. 25 : 4876-4882.Sequence alignment. http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html |
DAMBE
Xia X and Xie X (2001) Journal of heredity 92:371-373.Sequence alignment, phylogeny (distance, maximum likelihood, parsimony), graphic display of phylogenetic trees. http://dambe.bio.uottawa.ca/software.asp |
HYPHY
Kosakovsky Pond SL, Frost SDW and Muse SV (2005) Bioinformatics 21:676-679. Software package intended to perform maximum likelihood analyses of genetic sequence data with tools to test various statistical hypotheses. (OS X, Win, UNIX). http://www.hyphy.org/ |
MEGA
Kumar S, Tamura K and Nei M (1993) MEGA: Molecular Evolutionary Genetics Analysis, version 1.01. The Pennsylvania State University, PA.Phylogeny : disbtance, maximum likelihood, parsimony. http://www.megasoftware.net/ |
MESQUITE
Maddison WP and Maddison DR (2003) Mesquite: A modular system for evolutionary analysis, version 1.0.Software divided in modules for phylogenetic analysis, population genetics, while others do non-phylogenetic multivariate analysis. http://mesquiteproject.org/mesquite/mesquite.html |
MODELTEST
Posada D and Crandall KA (1998) Bioinformatics 14:817-818.Selection of a model of DNA substitution that best fits the data, among 56 possible models. This is accomplished through an implementation of hierarchical likelihood ratio tests and the AIC criterion. http://inbio.byu.edu/Faculty/kac/crandall_lab/Computer.html |
MRBAYES
Huelsenbeck JP (2000) MrBayes : Bayesian inferences of phylogeny (software). University of Rochester, NY.Bayesian estimation of phylogeny. http://mrbayes.csit.fsu.edu/index.php |
PAML
Yang Z (1997) CABIOS 13:555-556.Phylogenetic analyses of DNA or protein sequences using maximum likelihood. http://abacus.gene.ucl.ac.uk/software/paml.html |
PAUP
Swofford DL (2000) PAUP*: Phylogenetic analysis using parsimony and other methods (software). Sinauer Associates, Sunderland, MA.Hylogeny : distance, parsimony, and maximum likelihood. http://www.sinauer.com/detail.php?id=8060 |
PAUPRat
Sikes DS and Lewis PO (2001) beta software, version 1Program that generates a batch file for PAUP* to conduct a ratchet search. Strategy efficient at finding shortest trees for data sets too large for traditional heuristic search methods. (Mac, Win, UNIX). http://www.ucalgary.ca/~dsikes/software2.htm |
PHYLIP
Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington, Seattle.Phylogeny : distance, parsimony, and maximum likelihood. http://evolution.genetics.washington.edu/phylip.html |
POPULATIONS
Langella O (2001).Calculates individual- or population-based phylogenetic trees from a variety of genetic distance estimators; several bootstrapping options; can take GENEPOP of GENETIX formated files. http://bioinformatics.org/project/?group_id=84 |
PROSEQ
Filatov DA (2002) Molecular Ecology Notes 2:621-624Chromatogram viewer. Sequence editing (alignment), data import/export in various formats, population genetics analysis, phylogenetic analysis (neighbor-joining). http://helios.bto.ed.ac.uk/evolgen/filatov/proseq.html |
SplitsTree4
Huson DH and Bryant D (2006) Molecular Biology and Evolution 23:254-267.Provide framework for evolutionary analysis using both phylogenetic trees and networks. http://www.splitstree.org/ |
TCS
Clement M, Posada D and Crandall K (2000) Molecular Ecology 9:1657-1660.Collapse sequences, create a haplotype network (statistical parsimony). http://inbio.byu.edu/Faculty/kac/crandall_lab/Computer.html |
TRACER
Rambault A and Drummond A A program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes. (OS X, Win, Java). http://evolve.zoo.ox.ac.uk/software.html?id=tracer |
TREEVIEW
Page RDM (1996) Computer Applications in the Biosciences 12:357-358.Graphic display of phylogenetic trees. http://taxonomy.zoology.gla.ac.uk/rod/treeview.html |
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ASREML
Statistical package that fits linear mixed models using Residual Maximum Likelihood (REML). Usefull for using the « animal model » approach.http://www.vsni.co.uk/products/asreml/ |
Carthagene
Bouchez M, Chabrier P, de Givry S, Gaspin C and Schiex T.Genetic mapping software that handles several marker/family types. (PC) http://www.inra.fr/bia/T/CarthaGene/ |
Gmendel
Liu BH and Knapp SJ (1990) Journal of Heredity 81: 407Genetic linkage map construction and analyzing Mendelian phenotypes. Orders loci using data resampling methods (Monte Carlo and bootstrap sampling). (PC) http://cropandsoil.oregonstate.edu/G-mendel/Default.htm |
Mapmaker/EXP / Mapmaker/QTL
Lander and al. (1987) Genomics 1:174-181Genetic linkage analysis for dominant and codominant markers and a companion program (MAPMAKER/QTL) for mapping QTL underlying complex traits. (PC and Mac) ftp://ftp-genome.wi.mit.edu/distribution/software/mapmaker3 |
LinkMFex
Danzmann RGLinkage analysis for outcrossed families with male or female exchange of the mapping parent : allows analysis of segregation results from pairwise locus sets. (PC) http://www.uoguelph.ca/~rdanzman/software/LINKMFEX/ |
MapDisto
Lorieux MExcel Macro for mapping genetic markers Proposes recombination fraction estimates in cases of segregation distortion. (PC and Mac) http://mapdisto.free.fr/index.html |
PEST / VCE
Groeneveld EEstimation of genetic (co)variance of phenotype including heritability, genetic correlation and (EBV) estimated breeding values. Animal, sire and dam-based models are applicable (including sire-dam and animal-maternal systems). (PC) http://www.tzv.fal.de/~eg/ |
Qgene
Nelson JC (1997) Mol. Breed. 3: 239-245.Analysis of marker and phenotypic trait data in mapping families. (Mac) http://www.qgene.org/ |
QTL Cartographer
Basten CJ, Weir BS et Zeng ZB (2002) QTL Cartographer, Version 2.0 (Dec15). Department of Statistics, North Carolina State University, Raleigh, NC.Suite of programs to map quantitative traits using a map of molecular markers. Windows QTL Cartographer maps QTL in cross populations from inbred lines. Includes graphic tool for presenting results; import and export data in a variety of formats. Implement numerous methods: Single-marker, Interval mapping (Composite, Bayesian, Multiple), Multiple trait analysis. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm |
QTL express
Seaton G, Haley CS, Knott SA, Kearsey M and Visscher PM (2002) Bioinformatics 18:339-340.Web-based analysis of QTL from outbred populations. Includes tools for permutation analysis to set significance levels and bootstrap analysis to estimate confidence regions for the QTL location. (PC and Mac) http://qtl.cap.ed.ac.uk/ |
QTX
Manly KF, Cudmore Jr RH and Meer JM (2001) Mammalian Genome 12:930-932.QTL mapping through regression-based single locus association, simple interval mapping, composite interval mapping, and search for interacting QTL. (PC and Mac) http://www.mapmanager.org/mmQTX.html |
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Animal Genome Size Database
Database about the genome size of various animal species.http://www.genomesize.com |
Bgee
Database for gene expression evolution using homology relationships between anatomical structures of different species.http://bgee.unil.ch/bgee/bgee |
Bioinformatics journal - Next Generation Sequencing Tools list
Living ressource of tools developped with next generation sequencing applications in mind.http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html |
Blast2go
A universal gene ontology annotation, visualisation, and analysis tool for functional genomics research.http://www.blast2go.org/ |
CLC Genomic Workbench (CLC bio)
Powerful software solution for next-Generation sequencing data analysis.http://www.clcbio.com/index.php?id=1240 |
EMBL-EBI Portal (European Bioinformatic Institute)
Biological database (nucleotides, proteins, molecular interaction networks).http://www.ebi.ac.uk/Databases/ |
GeneOntology
Dictionary proposing a controlled vocabulary for organisms and gene and protein roles in cells.http://www.geneontology.org/ |
goldMiner
goldMINER automates functional annotation of unknown local and remote sequences
(ESTs and others) against pFAM and CDD (Conserved-Domain Database, which
integrates pFAM, SMART and COG, etc.) databases. Xuhua, X. Université d’Ottawa.http://dambe.bio.uottawa.ca/goldminer.asp |
Kegg Pathway Database
Current knowledge on molecular interaction networks, including metabolic pathways, regulatory pathways, and molecular complexes.http://www.genome.jp/kegg/pathway.html |
NCBI
Biological database (nucleotides, proteins, taxonomy), bioinformatic tools and GenBank portal.http://www.ncbi.nlm.nih.gov/ |
Reactome
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.http://www.reactome.org/ |
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ArcWeb Services
Searching too; for geographical coordinates in the world.http://arcweb.esri.com/services/placefinder/index.jsp |
Canadian Geographical Names Service (CGNS)
Searching tool for geographical coordinates in Canada.http://gnss.nrcan.gc.ca/ |
C-Squares
System for storage, querying and display of spatial data locations.http://www.marine.csiro.au/csquares/ |
Geographic Names Information System (GNIS)
Search ing tool for geographical cordinates in the United States.http://geonames.usgs.gov/ |
Pathmatrix
Ray, N. (2005). Molecular Ecology Notes, 5, 177-180.A tool used to compute matrices of effective geographical distances among samples using a least-cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. http://cmpg.unibe.ch/software/pathmatrix |
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Abbreviations - Journal Title
Abbreviations
List of scientific journal titles and their name's abbreviations. .http://www.bioscience.org/atlases/jourabbr/list.htm |
Allelogram
Software for normalizing and binning microsatellite genotypes. Manaster's home page. http://s92417348.onlinehome.us/index.html |
Applications - Canadian Spatial
Reference System
Online applications from the Canadian Spatial Reference System to convert
geographic coordinates (various formats).http://www.geod.nrcan.gc.ca/apps/index_e.php |
Conversion Programs
Convert .fsa files produced by an ABI® sequencer for use between Macintosh and PC platforms. (Mac)http://www.elimbio.com/file_conversion.htm |
Dropout
McKelvey, K.S. and Schwartz, M.K. (2005). Molecular Ecology Notes, 5, 716-718.MS-Windows program that identifies both loci and samples that likely contain genotyping errors affecting CMR estimates, in a capture-mark-recapture framework. http://www.fs.fed.us/rm/wildlife/genetics/ |
FREENA
CHAPUIS MP, ESTOUP A (2006) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol advanced online publication, December 5.PC computer program which estimates null allele frequencies for each locus and population analysed,estimates unbiased FST and computes a genotype dataset corrected for null alleles. http://www.montpellier.inra.fr/URLB/ |
Identity 1.0
Wagner, H.W. and Sefc, K.M. (1999). Centre for Applied Genetics, University of Agricultural Sciences, Vienna.This program offers 1) evaluation of microsatellite markers (diversity measures, etc), 2) detection of identical genotypes (synonyms) and 3) detection of possible parent-offspring combinations. http://www.boku.ac.at/zag/forsch/identity.htm |
ImageJ
Abramoff MD, Magelhaes PJ and Ram SJ (2004) Biophotonics International 11:36-42.Java image processing and analysis program. http://rsb.info.nih.gov/ij/ |
MARK
White, G.C. and Burnham, K.P. (1999). Bird Study (Supplement), 46, 120-138.Program MARK is a Windows-based program for analysis of data from marked individuals. A complete book describing all the applications of the program is available online and allows a better understanding of its different options. http://www.phidot.org/software/mark/docs/book/ |
Micro-Chercker
Van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M. and Shipley, P. (2004). Molecular Ecology Notes, 4, 535-538.Windows(R)-based software that aids identification of several kinds of genotyping errors in a microsatellite data set from diploid populations and corrects notably for null alleles. http://www.microchecker.hull.ac.uk/ |
PAST
Hammer Ø, Harper DAT et Ryan DP (2004)PAST is an easy data analysis package including common statistical, plotting and modelling functions. (Win) http://folk.uio.no/ohammer/past |
PGDSpider
Lischer HEL and Excoffier L (2012)Automated data conversion tool for population genetic and genomics http://www.cmpg.unibe.ch/software/PGDSpider/ |
Readseq
D.G. Gilbert, 2.1.30 (12-May-2010)Biosequence conversion tool http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi |
Sequence Analysis
©Informagen 2005Java application for conducting simple analysis on molecular sequences (e.g. pairwise comparisons, primer design, restrictions, etc…). (OS X) http://informagen.com/SA/ |
Statistical genetics - R packages
R packages implementing statistical methods and algorithms for the analysis of genetic data and for related population genetics studies. http://lib.stat.cmu.edu/R/CRAN/web/views/Genetics.html |
Termium
The government of Canada's terminology and linguistic database. Highly recommended for all your translation work.http://www.termium.com/site/termium.php?lang=eng&cont=001 |
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Bagel
Townsend, J.P., and D.L. Hartl. 2002. Bayesian
analysis of gene expression levels: statistical quantification of relative
mRNA level across multiple strains or treatments. Genome Biology 3
(12): research0071.1-0071.16.Bayesian analysis of replicated microarray data. http://web.uconn.edu/townsend/software.html |
Bioconductor (LIMMA)
Gentleman, Rossini, Dudoit and Hornik (2003)Microarray data analysis. Many of the software tools are general and can be used broadly for the analysis of genomic data, such as SAGE, sequence, or SNP data. http://www.bioconductor.org/ |
Cluster / Treeview
Eisen, MB, Spellman, PT, Brown, PO and D. Botstein. (1998)PNAS 95:14863 An integrated pair of programs for analyzing and visualizing the results of complex microarray experiments. http://rana.lbl.gov/EisenSoftware.htm |
David/EASE
Glynn Dennis Jr., Brad T. Sherman, Douglas A. Hosack, Jun Yang, Michael
W. Baseler, H. Clifford Lane, Richard A. Lempicki. DAVID: Database for
Annotation, Visualization, and Integrated Discovery. Genome Biology 2003
4(5): P3.DAVID and EASE provide integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. http://david.abcc.ncifcrf.gov/ |
ErmineJ
ErmineJ: Tool for functional analysis of gene expression data setsHomin K Lee, William Braynen, Kiran Keshav and Paul Pavlidis BMC Bioinformatics 2005, 6:269. ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. http://microarray.genomecenter.columbia.edu/ermineJ/ |
FATIGO
Al-Shahrour, F., Díaz-Uriarte, R. & Dopazo, J.FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.Bioinformatics 2004 20: 578-580. Microarray data mining and functional classification. http://fatigo.bioinfo.cipf.es/ |
GMEP
Chiang and al. (2001) Bioinformatics 17(suppl. 1):49-55.Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. http://rana.lbl.gov/EisenSoftware.htm |
Maanova
Wu H, Kerr MK, Cui X and Churchill GA (2002) Chapter of book The analysis of gene expression data: methods and software. Microarray data quality checks and visualization, transformation, ANOVA model fitting for both fixed and mixed effects models, statistical tests including permutation, confidence interval with bootstrapping, cluster analysis. http://www.jax.org/staff/churchill/labsite/software/ |
Onto-Express
Draghici, S., Khatri, P., Martins, R. P., Ostermeier, G. C., and Krawetz,
S. A. Global
functional profiling of gene expression. Genomics, 81: 98–104,
2003.Global functional profiling of microarray data. http://vortex.cs.wayne.edu/research.htm |
QVALUE
Storey JD. (2002) A direct approach to false discovery rates. Journal of
the Royal Statistical Society, Series B, 64: 479-498.Computes q-values for a set of p-values in the R environment. http://faculty.washington.edu/~jstorey/qvalue/ |
SAM
Tusher, Tibshirani and Chu (2001) PNAS 98: 5116-5121.Analyses for micro-array data. modified t-tests and permutation tests. http://www-stat.stanford.edu/~tibs/SAM/ |
SAS
© SAS institute incGibson G. Manual for Mixed Model Analysis of Microarray Data (MANMADA). http://statgen.ncsu.edu/ggibson/gibson_website/Manual.html |
Scanalyse
Eisen M (2002)Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. http://rana.lbl.gov/EisenSoftware.htm |
SMA
Dudoit S, Yang YH, Callow M and Speed T (2000) Technical Report.Groupe de fonctions programmées dans R pour l’analyse statistique des données de plusieurs bio-puces. http://stat-www.berkeley.edu/users/terry/zarray/Software/smacode.html |
Vera et Sam
Ideker T, Thorsson V, Siegel AF and Hood L (2000) Journal of Computational Biology 7:805-817Estimate error model parameters from replicated microarray experiments results. Use error model to improve the accuracy of the expression ratio. http://db.systemsbiology.net/software/VERAandSAM/ |
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