How to use GeneClass2
?
Standard disclaimer: This
program is provided "as-is". The authors and providers disclaim all warranties,
expressed or implied, regarding the performance of this software. You may distribute
this program freely in any format, so long as the following conditions are met:
the program remains intact without modification, the help file is included without
modification, no fee of any kind is charged.
Please cite this
reference if you use GeneClass2:
Piry S, Alapetite
A, Cornuet, J.-M., Paetkau D, Baudouin, L., Estoup, A. (2004) GeneClass2:
A Software for Genetic Assignment and First-Generation Migrant Detection.
Journal of Heredity 95:536-539.
WARNING: For reasons of international compatibility,
the decimal separator used in GeneClass2 is a dot ".".
In order to use GeneClass2, your dataset(s) must be in a recognizable format.
The file formats that are recognized are: GenePop
(alleles coded with 2 or 3 digits, or haploid) (Raymond
& Rousset, 1995; see also "Genepop
on the web"), FStat
(Goudet, 1995), Genetix
(Belkhir et al.), plus a XML (eXtended Markup
Language) based format and an internally-used format (CIRAD-PRN). Please consult
these references for detailed information on the file formats.
Note that it is preferable that the datafile contains as few missing data as
possible (see Piry et al., 2004 for missing data
management).
The language (French or English) can be choosen with the "Language"
menu of GeneClass2.
It is worth noting that for most options chosen in the program
a reference is indicated in a window: it is recomended to consult such references
when detailed information are needed.
The following links provide more detailed instructions on the
use of GeneClass2.
- Detection of migrants
- Assignment of individuals (or groups of individuals)
- Data file conversion and description of population diversity
Bibliography
- Baudouin L, Lebrun P (2000)
An operational bayesian approachfor the identification of sexually reproduced
cross-fertilized populations using molecular markers. Acta Horticulturae
546, 81-93.
- Belkhir K, Borsa P, Chikhi L,
Raufaste N, Bonhomme F (1996-2001) GENETIX 4.02, logiciel sous Windows TM
pour la génétique des populations, Laboratoire Génome,
Populations, Interactions; CNRS UMR 5000; Université Montpellier II,
Montpellier (France).
- Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic
analysis: models and estimation procedures. American Journal of Human
Genetics 19, 233-257.
- Cornuet JM, Piry S, Luikart G, Estoup A, Solignac
M (1999) New methods employing multilocus genotypes to select or exclude populations
as origins of individuals. Genetics 153, 1989-2000.
- Goldstein DB, Ruiz Linares A, Cavalli-Sforza
LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and
the origin of modern humans. Proceedings of the National Academy of Sciences
USA 92, 6723-6727.
- Goudet J (1995) Fstat version 1.2: a computer
program to calculate Fstatistics. Journal of Heredity 86,
485-486.
- Nei M (1972) Genetic distance between populations.
American Naturalist 106, 283-291.
- Nei M (1973) The theory and estimation of genetic
distances. In: Genetic Structure of Populations (ed. Morton NE).
University Press of Hawaii, Honolulu.
- Nei M (1987) Molecular Evolutionary Genetics
Columbia University Press, New-York.
- Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated
phylogenetic trees from molecular data. Journal of Molecular Evolution
19, 153-170.
- Paetkau D, Calvert W, Stirling I, Strobeck C
(1995) Microsatellite analysis of population structure in Canadian polar bears.
Molecular Ecology 4, 347-354.
- Paetkau D, Slade R, Burden M, Estoup A (2004)
Direct, real-time estimation of migration rate using assignment methods: a
simulation-based exploration of accuracy and power. Molecular Ecology
13:55-65.
- Paetkau D, Waits LP, Clarkson PL, Craighead L,
Strobeck C (1997) An empirical evaluation of genetic distance statistics using
microsatellite data from bear (Ursidae) populations. Genetics 147:1943-1957.
- Piry
S, Alapetite A, Cornuet, J.-M., Paetkau D, Baudouin, L., Estoup, A. (2004)
GeneClass2: a software for genetic assignment and first generation migrants
detection. Journal of Heredity 95:536-539.
- Rannala B, Mountain JL (1997) Detecting immigration
by using multilocus genotypes. Proceedings of the National Academy of
Sciences USA 94, 9197-9201.
- Raymond M, Rousset F (1995) GENEPOP (version
1.2): population genetics software for exact tests and ecumenicism. Journal
of Heredity 86, 248-249.
- Takezaki N, Nei M (1996) Genetic Distances and
Reconstruction of Phylogenetic Trees from Microsatellite DNA. Genetics
144, 389-399.