SPAGeDi 1.5a – Spatial Pattern Analysis of Genetic Diversity

SPAGeDi 1.5a

:: DESCRIPTION

SPAGeDi (Spatial Pattern Analysis of Genetic Diversity) is a computer package primarily designed to characterise the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.

::DEVELOPER

Olivier Hardy and Xavier Vekemans @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SPAGeDi

:: MORE INFORMATION

Citation:

Hardy OJ, Vekemans X (2002)
SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels.
Molecular Ecology Notes 2: 618-620.

AQUASPLATCHE 1.0 – Simulate Genetic Diversity based on a Realistic Vectorized Environment

AQUASPLATCHE 1.0

:: DESCRIPTION

AQUASPLATCHE starts by dividing a realistic vectorized network of river streams into segments of arbitrary length. The program then proceeds by simulating the colonization of the streams from an arbitrary source, recording the evolution of the segment densities and the migration events between adjacent segments over time. This demographic history is then used to generate genetic data of population samples located in various segments of the river system, using a backward coalescent framework.

::DEVELOPER

Samuel NeuenschwanderComputational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 AQUASPLATCHE

:: MORE INFORMATION

Citation

Neuenschwander S (2006)
AQUASPLATCHE: a program to simulate genetic diversity in populations living in linear habitats.
Molecular Ecology Notes 6 583-585.

DemoDivMS 0.2 – Predict Genetic Diversity at Microsatellite DNA Marker

DemoDivMS 0.2

:: DESCRIPTION

DemoDivMS is designed to predict the genetic diversity at a microsatellite DNA marker, in a finite population, for various mutation models and for variable population size.

::DEVELOPER

N. Nikolic(contact author), INRA / C. Chevalet 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Fortran

:: DOWNLOAD

  DemoDivMS

:: MORE INFORMATION

References

Nikolic N, Butler J, Baglinière J-L, Laughton R, McMyn I.A.G, Chevalet C. 2009.
An examination of genetic diversity and effective population size in Atlantic salmon.
Genetics Research. 91: 1-18.

AFLPsurv 1.0 – Genetic Diversity Analysis with AFLP (and RAPD) Population data

AFLPsurv 1.0

:: DESCRIPTION

AFLP-SURV estimates genetic diversity and population genetic structure from population samples analysed with AFLP or RAPD methods and computes geneitc distance matrices between populations. The program starts by estimating allelic frequencies at each marker locus in each population assuming they are dominant and have only two alleles (a dominant marker allele coding for the presence of a band at a given position and a recessive null allele coding for the absence of the band).

::DEVELOPER

Xavier Vekemans @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AFLPsurv

:: MORE INFORMATION

pim 0.3 – Alignment-free Estimation of Genetic Diversity

pim 0.3

:: DESCRIPTION

pim is a program for efficiently estimating the number of mismatches between a pair of unaligned sequences

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 pim

:: MORE INFORMATION

Citation

B. Haubold, F. A. Reed, and P. Pfaffelhuber.
Alignment-free estimation of nucleotide diversity.
Bioinformatics, doi: 10.1093/bioinformatics/btq689, 2010.

CFC 1.0 – Monitor Genetic Diversity

CFC 1.0

:: DESCRIPTION

CFC is originally developed to compute population statistics on relationships by a computationally efficient indirect method.

::DEVELOPER

Mehdi Sargolzaei

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CFC

:: MORE INFORMATION

Citation

Sargolzaei, M., H. Iwaisaki and J.J. Colleau. 2006.
CFC: A tool for monitoring genetic diversity.
Proc. 8th World Congr. Genet. Appl. Livest. Prod., CD-ROM Communication 27-28. Belo Horizonte, Brazil, Aug. 13-18, 2006.