BIODIVERSITY AND CONSERVATION
NATIONAL
INTERNATIONAL
 
OTHERS LABS
OUR RECENT AND CURRENT COLLABORATORS
OTHERS RESEARCHERS STUDYING FISH GENETICS AND EVOLUTIONARY BIOLOGY
 
PARENTAGE AND RELATEDNESS ANALYSES
POPULATION ASSIGNMENT, ADMIXTURE, HYBRIZATION
POPULATION STRUCTURE AND PARAMETERS
PHYLOGENETIC ANALYSES, SEQUENCE ALIGNEMENT
QUANTITATIVE GENETICS AND GENOME-QTL MAPPING
GENOMICS
GEOGRAPHIC TOOLS
UTILITIES
MICROARRAYS

 

BIODIVERSITY AND CONSERVATION

NATIONAL

L’Action Boréale in Abitibi-Témiscamingue (president: Richard Desjardins).
http://www.actionboreale.qc.ca/
Information on research, conservation and aquatic biodiversity in Canada.
http://www.aquatic.uoguelph.ca/
Applied research focusing on rivers ecosystems.
http://www.unb.ca/cri
Committee on the status of endangered wildlife in Canada.
http://www.cosewic.gc.ca/index.htm
Environment Canada.
http://www.ec.gc.ca/
Québécois Coalition for responsible management of water resources.
http://www.eausecours.org/
Non-profit organisation dedicated to the protection of biodiversiy in Quebec.
http://www.fondationdelafaune.qc.ca/
The Group for research and eduction on marine mammals.
http://www.gremm.org/
Richesses Naturelles et Faune Québec.
http://www.mrnfp.gouv.qc.ca/
A beer for threatened species.
http://www.rescousse.qc.ca/
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INTERNATIONAL

http://www.cites.org/
Endangered Species Act (USA).
http://endangered.fws.gov/esa.html
Food and Agriculture Organization of the United Nations.
http://www.fao.org/
Site dedicated to the world fish biodiversity (28 100 fish species, 35 300 photos).
http://www.fishbase.org/search.html
For chosing the right seafood and fish to eat.
http://www.mbayaq.org/
Organization that promotes the protection of biodiversity and an equitable use of natural resources.
http://www.iucn.org/
Threatened species of the world.
http://www.unep-wcmc.org
http://endangered.fws.gov/
http://www.wri.org/
Fonds Mondial pour la Nature.
http://www.wwf.ca/
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OTHERS LABS

OUR RECENT AND CURRENT COLLABORATORS

ISMER, l’Institut des Sciences de la Mer de Rimouski.
Université du Québec à Rimouski, Québec, Canada
http://www.pqm.net/ismer/index.html
Maine Department of Inland Fisheries and Wildlife
Dept. of Biological Sciences, Macquarie University
Sydney, Australia
http://www.bio.mq.edu.au/molecularecology/
Université de Montréal, Québec, Canada
http://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
Université du Québec à Rimouski, Québec, Canada
http://www.uqar.qc.ca/bcss/bio/Personnel/PBlier1.htm
Université de Sherbrooke, Québec Canada &
Québec-Océan, Le Groupe interinstitutionnel de recherches océanographiques du Québec
Université Laval, Québec, Canada
http://www.usherbrooke.ca/
INRS, Eau, terre et environnement
http://www.ete.inrs.ca/peter-gc-campbell
Ressources naturelles et Faune Québec (MRNF), Québec
http://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
Département de biologie
Université 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
INRS Eau, Terre & Environnement
http://www.ete.inrs.ca/patrice-couture
INRS-Institut Armand Frappier.
http://www.iaf.inrs.ca/daniel-g-cyr
University of Guelph, ON, Canada
http://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
Département de biologie
Université 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/
Ressources naturelles et Faune Québec (MRNF), Québec
http://www.fapaq.gouv.qc.ca/
NINA Norwegian Institute for Nature Research, Norway
http://www.nina.no
Département de biologie, Université de Sherbrooke.
http://www.usherbrooke.ca/biologie/personnel/professeurs/ecologie-terrestre/dany-garant/
Département de biologie
Université 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
Département de biologie
Université 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/
Dannish Institute of Fisheries Research, Denmark
http://www.aqua.dtu.dk/English.aspx
Department of Intergrative Biology, University of Guelph, Guelph.
http://www.uoguelph.ca/~phebert/
NINA Norwegian Institute for Nature Research, Norway
http://www.nina.no
Department of Biology, Dalhousie university.
http://biology.dal.ca/People/faculty/hutchings/hutchings.htm
Institute of Freshwater Fisheries
Holar, Iceland
http://www.veidimal.is/
Leetown Science Center, USGS
http://www.lsc.usgs.gov/

Roger Lévesque
Director, Institut de Biologie Intégrative et des Systèmes (IBIS)
Researcher, Molecular microbiology and protein engineering, Université Laval
http://rclevesque.rsvs.ulaval.ca/

Biology Departement
Saint-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
Ressources naturelles et Faune Québec (MRNF), Québec
http://www.fapaq.gouv.qc.ca/
Department of Fisheries and Oceans
Pacific 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
NINA Norwegian Institute for Nature Research, Norway
http://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
Estacion Biologia de Donana, Sevilla, Espana
http://www.ebd.csic.es/
ISCF, Service Canadien de la Faune
Québec, Canada
http://www.ec.gc.ca/
Ressources naturelles et Faune Québec (MRNF), Québec
http://www.fapaq.gouv.qc.ca/
Molecular Ecology and Fisheries Genetics Laboratory
Univerity of Hull, U.K.
http://www.hull.ac.uk/biosci/staff/academic/MolecularEcologyandEvolution/GeorgeTurner.html
Département de biologie
Université 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
Department of Biology
University of Oslo
http://www.bio.uio.no/akv/english/staff/biography/vollestad_Asbjorn.html
Department of Zoology
University of Otago, Dunedin, New Zealand
http://www.otago.ac.nz/Zoology/staff/otago008937.html
CNRS, Centre d’Études Biologiques de Chizé, France
http://www.cebc.cnrs.fr/
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OTHERS RESEARCHERS STUDYING FISH GENETICS AND EVOLUTIONARY BIOLOGY

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
DFO Chair, Fisheries Resource Conservation
Dalhousie University, N.S. Canada
http://biology.dal.ca/People/faculty/bentzen/bentzen.htm
Molecular Ecology and Evolution of Fishes
University 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
Génome, Populations Interactions Adaptation
Université de Montpellier, France
http://www.univ-montp2.fr/%7Egenetix/index.htm#thema
Hawaii Institute of Marine Biology, U.S.A.
http://www.hawaii.edu/HIMB/
Molecular Ecology and Fisheries Genetics Laboratory
Univerity of Hull, U.K.
http://www.hull.ac.uk/molecol/index.html
South Carolina Department of Natural Resources
www.marinegenomics.org
Great Lakes Institute for the Environment
University of Winsdor, ON, Canada
http://cronus.uwindsor.ca/units/glier/NewMain.nsf/inToc/560038DDEA988E2185256E5900527CC3
Redpath Museum
McGill University, Québec, Canada
http://ww2.mcgill.ca/biology/faculty/hendry/
Senior Research Fellow
Institute of Zoology, London, UK.
http://www.zoo.cam.ac.uk/ioz/index.htm
Genome Evolution Center
Stanford University, U.S.A.
http://cegs.stanford.edu/index.jsp
University of Maine, U.S.A.
http://biology.umaine.edu/
Hubbard Center for Genome Studies
University of New Hampshire, U.S.A.
http://hcgs.unh.edu/
GRASP (Genomic Research on Atlantic Salmon Project)
University of Victoria, B.C., Canada
http://web.uvic.ca/cbr/grasp/
University of Konstanz, Germany
http://www.evolutionsbiologie.uni-konstanz.de/
Department of Biology
University of Western Ontario, ON, Canada
http://www.uwo.ca/biology/Faculty/neff/index.htm
Department of Biology at the University of Turku, Finland
http://users.utu.fi/primmer/
Beren Robinson
Deaprtment of Integrative Biology, University of Guelph
http://www.uoguelph.ca/ib/faculty/faculty_robinson.shtml
Canadian Research Chair in Marine Conservation Genetics
Dalhousie University, N.S., Canada
http://biology.dal.ca/us/f/ruzzante/ruzzante.htm
University of British Columbia, B.C., Canada
http://www.zoology.ubc.ca/~schluter/
Molecular Ecology Laboratory
Michigan State University, U.S.A.
http://www.fw.msu.edu/people/ScribnerKim/
UBC Center for Biodiversity Research
University of British Columbia, B.C., Canada
http://www.zoology.ubc.ca/~etaylor/index.html
Lab. Aquatische ecologie, Leuven, Belgium
http://cwisdb.cc.kuleuven.be/persdb-bin/persdb
Northwest Fisheries Science Center, U.S.A
http://www.nwfsc.noaa.gov/
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SOFTWARES, DATABASES AND OTHER INTERNET RESOURCES

PARENTAGE AND RELATEDNESS ANALYSES

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
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
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
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
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
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
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/
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
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
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
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/
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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POPULATION ASSIGNMENT, ADMIXTURE, HYBRIZATION

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/
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
Coriander J, Waldmann P and Sillanpää MJ (2003) Genetics 163:367-374
Bayesian 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
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
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
Rosenberg NA (2004) Molecular Ecology Notes 4:137-138
Enables graphical display of Structure output and allows for additional optional files.
http://rosenberglab.bioinformatics.med.umich.edu/software.html
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
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/
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
Rannala B and Mountain JL (1997) PNAS 94: 9197-9201.
Detects immigrants using multilocus genotypes.
http://www.rannala.org/labpages/software.html
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
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
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
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
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
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 ***
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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POPULATION STRUCTURE AND PARAMETERS

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
Schneider S, Roessli D and Excoffier L (2000) University of Geneva, Switzerland
Software for population genetics data analysis, including genetic differentiation and analyses of molecular variance (AMOVA).
http://lgb.unige.ch/arlequin/
Manni F, Guérard E and Heyer E (2004) Human Biology 76:173-190
Computes 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
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/
Gaggiotti OE, Brooks SP, Amos W and Harwood J (2004) Molecular Ecology 13: 811-825
Software 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
Glaubitz JC (2004) Molecular Ecology Notes 4:309-310
A 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
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
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/
Balloux F, Brünner H, Lugon-Moulin N, Hausser J and Goudet J (2000) Evolution 54:1414-1422
A simulation software for population genetics.
http://www.unil.ch/dee/page6759.html
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/
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
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
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 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
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
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/
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
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
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
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/
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
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
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
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
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
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
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
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
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
Molecular Fisheries Laboratory, Queensland, Australia
Methods for estimating Ne from three different temporal methods.
http://www2.dpi.qld.gov.au/fishweb/13887.html
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/
Holsinger KE and Mason-Gamer RJ (1996) Genetics 142:629-639.
Hierarchical analysis of nucleotide diversity between populations.
http://darwin.eeb.uconn.edu/#software
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
Yeh F, Yang R and Boyle T (2001) University of Alberta
Analysis of genetic variation among and within populations.
http://www.ualberta.ca/~fyeh/index.htm
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
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/
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
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
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
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
Mark Miller (1997) Utah State University
Tools for population genetics analysis.
http://bioweb.usu.edu/mpmbio/index.htm
Berthier P, Beaumont MA, Cornuet J-M and Luikart G (2002) Genetics 160:741-751
Maximum-likelihood estimation of effective population size (using temporal method).
http://www.rubic.rdg.ac.uk/%7emab/software.html
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PHYLOGENETIC ANALYSES, SEQUENCE ALIGNEMENT

Java application for the visualization of annotated phylogenetic trees.
http://www.phylosoft.org/archaeopteryx/
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/
Hall TA (1999) Nucl. Acids. Symp. Ser. 41:95-98
Sequence editor.
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
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
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
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/
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/
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
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
Huelsenbeck JP (2000) MrBayes : Bayesian inferences of phylogeny (software). University of Rochester, NY.
Bayesian estimation of phylogeny.
http://mrbayes.csit.fsu.edu/index.php
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
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
Sikes DS and Lewis PO (2001) beta software, version 1
Program 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
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
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
Filatov DA (2002) Molecular Ecology Notes 2:621-624
Chromatogram 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
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/
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
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
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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QUANTITATIVE GENETICS AND GENOME-QTL MAPPING

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/
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/
Liu BH and Knapp SJ (1990) Journal of Heredity 81: 407
Genetic 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
Lander and al. (1987) Genomics 1:174-181
Genetic 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
Danzmann RG
Linkage 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/
Lorieux M
Excel Macro for mapping genetic markers Proposes recombination fraction estimates in cases of segregation distortion. (PC and Mac)
http://mapdisto.free.fr/index.html
Groeneveld E
Estimation 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/
Nelson JC (1997) Mol. Breed. 3: 239-245.
Analysis of marker and phenotypic trait data in mapping families. (Mac)
http://www.qgene.org/
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
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/
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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GENOMICS

Database about the genome size of various animal species.
http://www.genomesize.com
Database for gene expression evolution using homology relationships between anatomical structures of different species.
http://bgee.unil.ch/bgee/bgee
Living ressource of tools developped with next generation sequencing applications in mind.
http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html
A universal gene ontology annotation, visualisation, and analysis tool for functional genomics research.
http://www.blast2go.org/
Powerful software solution for next-Generation sequencing data analysis.
http://www.clcbio.com/index.php?id=1240
Biological database (nucleotides, proteins, molecular interaction networks).
http://www.ebi.ac.uk/Databases/
Dictionary proposing a controlled vocabulary for organisms and gene and protein roles in cells.
http://www.geneontology.org/
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
Current knowledge on molecular interaction networks, including metabolic pathways, regulatory pathways, and molecular complexes.
http://www.genome.jp/kegg/pathway.html
Biological database (nucleotides, proteins, taxonomy), bioinformatic tools and GenBank portal.
http://www.ncbi.nlm.nih.gov/
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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GEOGRAPHIC TOOLS

Searching too; for geographical coordinates in the world.
http://arcweb.esri.com/services/placefinder/index.jsp
Searching tool for geographical coordinates in Canada.
http://gnss.nrcan.gc.ca/
System for storage, querying and display of spatial data locations.
http://www.marine.csiro.au/csquares/
Search ing tool for geographical cordinates in the United States.
http://geonames.usgs.gov/
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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UTILITIES

List of scientific journal titles and their name's abbreviations. .
http://www.bioscience.org/atlases/jourabbr/list.htm
Software for normalizing and binning microsatellite genotypes.
Manaster's home page.
http://s92417348.onlinehome.us/index.html
Online applications from the Canadian Spatial Reference System to convert geographic coordinates (various formats).
http://www.geod.nrcan.gc.ca/apps/index_e.php
Convert .fsa files produced by an ABI® sequencer for use between Macintosh and PC platforms. (Mac)
http://www.elimbio.com/file_conversion.htm
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/
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/
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
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/
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/
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/
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
Lischer HEL and Excoffier L (2012)
Automated data conversion tool for population genetic and genomics
http://www.cmpg.unibe.ch/software/PGDSpider/
D.G. Gilbert, 2.1.30 (12-May-2010)
Biosequence conversion tool
http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi
©Informagen 2005
Java application for conducting simple analysis on molecular sequences (e.g. pairwise comparisons, primer design, restrictions, etc…). (OS X)
http://informagen.com/SA/
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
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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MICROARRAYS

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
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/
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
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: Tool for functional analysis of gene expression data sets
Homin 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/
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/
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
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/
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
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/
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 institute inc
Gibson G. Manual for Mixed Model Analysis of Microarray Data (MANMADA).
http://statgen.ncsu.edu/ggibson/gibson_website/Manual.html
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
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
Ideker T, Thorsson V, Siegel AF and Hood L (2000) Journal of Computational Biology 7:805-817
Estimate 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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