Populations 1.2.28 (12/5/2002)
Population genetic software (individuals or
populations distances, phylogenetic trees)
Contents
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Populations, 1.2.28 (12/5/2002) 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, CNRS UPR9034
Debian GNU/Linux package : populations_1.2.28-1_i386.deb
RPM GNU/Linux package (RedHat ou Mandrake) : populations-1.2.28-2.i386.rpm
Sources : populations-1.2.28.tar.gz
Windows :
populations.exe
to compile "populations", download tar.gz sources an
do the following with root privileges:
tar xvfz populations-1.2.28.tar.gz
cd populations-1.2.28
./configure
make
make install
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)
Rogers', 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
- output
input files
"Populations" accepts file from other population
genetic softwares:
- Genepop
- Génétix
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
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.
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