Populations

# Populations 1.2.31

Population genetic software (individuals or populations distances, phylogenetic trees)

- Contents
- Download
- Distances
- File formats
- Command line
- Bibliography
- Formula

## 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

### all systems

download populations

### Ubuntu packages

If you are using Ubuntu, you can find "populations" and "treeplot" packages here :
https://launchpad.net/~olivier-langella/+archive
Please modify your source list entries to add the repositorie that corresponds to your Ubuntu version ( Adding Repositories in Ubuntu how to )

## 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
- 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:
Genepop
Génétix
Populations
Lea
Immanc
microsat
Admix (G. Bertorelle)
Fstat (Jerome Goudet)
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.