Populations 1.2.31
Population genetic software (individuals
or populations distances, phylogenetic trees)
Contents
- haploids, diploids or polyploids genotypes (see input formats)
- structured populations (see input files structured populations
- No limit of populations, loci, alleles per loci (see input formats)
- Distances between individuals (15 different methods)
- Distances between populations (15 methods)
- Bootstraps on loci OR individuals
- Phylogenetic trees (individuals or populations), using
Neighbor Joining or UPGMA (PHYLIP tree format)
- Allelic diversity
- Converts data files from Genepop to different formats
(Genepop, Genetix, Msat, Populations...)
Download
Populations, 1.2.30 Copyright (C) 1999,
Olivier Langella, CNRS UPR9034
This program is free software; you can
redistribute it and/or modify it under the terms of the
GNU General Public
License as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version licence
This program is distributed in the hope
that it will be useful,but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the
GNU General
Public License for more details.
You should have received a copy of the GNU
General Public License along with this program; if not, write to the
Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
02111-1307, USA.
Authors
Olivier Langella
Distances
- DAS, shared allele distance
(Chakraborty et Jin., 1993)
- Nei, minimum genetic
distance, Dm (Nei,1987)
- Nei, standard genetic
distance, Ds (Nei, 1987)
- Cavalli-Sforza
and Edwards, Dc (1967)
- Nei et al's, DA
(1983)
- Latter, Fst (1972)
- Prevosti et al.'s, Cp
(1975)
- Roger's, Dr (1972)
- Reynolds J.
unweighted, Dru (1983)
- Reynolds J.
weighted, Drw (1983)
- Reynolds
J. least squares, Drl (1983)
- Microsatellites distances
- Goldstein et al., dmu2 (1995a)
- Average Square Distance ( ASD , Goldstein, Slatkin 1995)
- Shriver et al's, Dsw (1995)
- Lev A. Zhivotovsky, DR (1999)
Formats
input files
"Populations" accepts file from other
population genetic softwares:
and it has its own format:
"Populations" format allows to use unlimited number of alleles, of
haploids, diploids or nploids. The format is close to Genepop but
alleles at a given locus are separated by ":". Thus, man can code
alleles with all ASCII characters.
Diploid population example:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02:01 03:03 01:02 03:02 10:11
Montpellier2 , 02:02 03:01 01:02 03:03 11:11
Montpellier3 , 01:02 04:01 02:02 01:02 10:10
Montpellier4 , 01:03 02:02 01:01 02:02 10:11
Montpellier5 , 02:03 02:04 01:01 01:02 10:10
POP Gigondas
Gigondas1 , 01:02 02:02 02:01 04:05 08:07
Gigondas2 , 01:02 02:01 02:01 04:05 03:07
Gigondas3 , 02:01 02:03 01:01 05:05 04:02
Gigondas4 , 02:01 03:03 03:01 03:03 06:03
Gigondas5 , 01:01 02:01 03:01 05:05 08:07
Haploid example :
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02 03 01 03 10
Montpellier2 , 02 03 01 03 11
Montpellier3 , 01 04 02 01 10
Montpellier4 , 01 02 01 02 10
Montpellier5 , 02 02 01 01 10
POP Gigondas
Gigondas1 , 01 02 02 04 08
Gigondas2 , 01 02 02 04 03
Gigondas3 , 02 02 01 05 04
Gigondas4 , 02 03 03 03 06
Gigondas5 , 01 02 03 05 08
example of haploid, using any ASCII
character: no space in allele names:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , all2 03 01 03 10
Montpellier2 , all2 03 01 03 11
Montpellier3 , all1 04 02 01 miss
Montpellier4 , all1 02 01 02 10
Montpellier5 , all2 02 01 01 10
POP Gigondas
Gigondas1 , all1 02 02 04 08
Gigondas2 , all1 02 02 04 miss
Gigondas3 , all2 02 01 05 04
Gigondas4 , all2 03 03 03 06
Gigondas5 , all1 02 03 05 08
Structured population
To code metapopulations, you can choose
either "Genepop" or "Populations" format. You only need to give the name
of population after the keyword "POP " (separator = "/")
example:
exemple de populations structurées
locus1
locus2
locus3
POP Rennes/immeuble_sud/pop_3emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
POP Rennes/immeuble_sud/pop_2emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
Output files
Populations is able to produce various
population genetic software formats:
Populations
Lea
microsat
Phylogenetic trees are coded using the
"Phylip" format. "
Treeview"
can be used for Windows or Linux, and you can use ">Treeplot" to convert
the phylip format into postscript, adobe illustrator, gif... with colors
for each populations
Matrix distances files are "Excel
(gnumeric compatible)", "Phylip", "xgobi", "NTsys" or any text editor
compliant.
Command line
You can use "Populations" as a command
line programm (very useful for batch treatment) to infer phylogenetic
trees:
populations name_of_input_file -"arguments"
Available arguments:
-phylogeny ind ou pop (default) for
phylogenetic trees based on individuals or populations
-dist method (default: Nei standard, Ds)
you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw,
Dr, Dru, Drw, Drl. see distances for details.
-construct method (default: upgma)
possibilities upgma or nj (Neighbor Joining)
-bootstrap_ind number to indicate the
number of bootstraps to perform on individuals
-bootstrap_locus number to indicate the
number of bootstraps to perform on loci
-output name_of_treeview_file to indicate
the name of the tree file (phylip tree format)
-level number , structured populations
allows to choose the structuration factor (in the example: town level is
1, building level is 2...).
example:
populations toutc2.txt -phylogeny pop -dist Dm
-bootstrap_locus 10000 -output toutc2_10000_Dm.tre
Commands can be write in a .bat file (for
DOS) or a script file (for UNIX).
Bibliography
Bruce Ranala and Joanna L.
Mountain. Detecting immigration by using multilocus genotypes.
Proc.Natl. Acad. Sci. USA, 94:9197-9201, 13/6/1997.
David B. Goldstein, Andres
Ruiz Linares, Luigi Luca Cavalli-Sforza and Marcus W. Feldman. An
Evaluation of Genetic Distances for Use With Microsatellite Loci.
Genetics, 139:463-471, 5/10/1994.
D. B. Goldstein and D. D.
Pollock. Launching Microsatellites: A Review of Mutation Processes and
Methods of Phylogenetic Inference. Journal of Heredity,
88(335-342):0022-1503, 31/3/1997.
Li Jin and
Ranajit Chakraborty. Estimation of Genetic Distance and Coefficient of
Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data.
Mol. Biol. Evol, 11(1):120-127, 13/9/1993.
Mark D. Shriver, Li Jin,
Eric Boerwinkle, Ranjan Deka, Robert E. Ferrel and Ranajit Chakraborty.
A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat
Loci. Mol. Biol. Evol, 12(5):914-920, 13/4/1995.
Montgomery Slatkin. A
Measure of Population Subdivision on Microsatellite Allele Frequencies.
Genetics, (139):457-462, 19/6/1994.
Naruya Saitou and Masatoshi
Nei. The Neigbhor-joining Method: A New Method for Reconstructing
Phylogenetic Trees. Mol. Biol. Evol, 4(4):406-425, 18/2/1987.
Naoko Takezaki and Masatoshi
Nei. Genetic Distances and Reconstruction of Phylogenetic Trees From
Microsatellite DNA. Genetics, (144):189-399, 6/6/1996.
William J. Bruno, Nicholas
D. Socci and Aaron L. Halpern. Weighted Neigbhor Joining: A
Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction.
Mol. Biol. Evol, 17(1):189-197, 11/10/1999.