:: DESCRIPTION
CFC is originally developed to compute population statistics on relationships by a computationally efficient indirect method.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
SPLATCHE (for SPatiaL And Temporal Coalescences in Heterogenous Environment) is a program that allows to incorporate the influence of environment in the simulation of migration of a given species from one origin. In a second phase, the molecular genetic diversity of one or several samples drawn from the simulated species can be generated.
::DEVELOPER
Computational and Molecular Population Genetics Lab, University of Bern
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N.
SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.
Bioinformatics. 2019 Nov 1;35(21):4480-4483. doi: 10.1093/bioinformatics/btz311. PMID: 31077292; PMCID: PMC6821363.
Ray N, Currat M, Foll M, Excoffier L. (2010)
SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination.
Bioinformatics, Volume 26, Issue 3, Page 2993-2994.
:: 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 @ the unit of Evolutionary Biology & Ecology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
Computational and Molecular Population Genetics Lab, University of Bern
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
pim is a program for efficiently estimating the number of mismatches between a pair of unaligned sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
B. Haubold, F. A. Reed, and P. Pfaffelhuber.
Alignment-free estimation of nucleotide diversity.
Bioinformatics, doi: 10.1093/bioinformatics/btq689, 2010.
