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Liste des programmes:
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fastsimcoal2:
a much faster continuous-time implementation of simcoal2, based on a
sequential Markovian coalescent approximation, allowing it to
efficiently generate genetic diversity along large genomic regions under
complex evolutionary histories, and this for for both present or
ancient samples. New version (2.0) is available.
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BayeScan: a software to detect natural selection from population-base genetic data. New version (2.0) is available.
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Arlequin: an integrated software package for population genetics data analysis. New version (3.5) is available
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SPLATCHE: A program to simulate genetic diversity taking into account environmental heterogeneity.
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SIMCOAL2:
a general coalescent program to simulate genomic diversity over large
recombining regions in a subdivided population with a complex history
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ABCtoolbox:
a versatile toolkit to perform Approximate Bayesian Computations (ABC)
using various recently published algorithms including MCMC without
likelihood, Population Monte Carlo and ABC-GLM.
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SAMOVA:
a program that implements an approach to define groups of populations
that are geographically homogeneous and maximally differentiated from
each other.
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AQUASPLATCHE: a program to simulate genetic diversity based on a realistic vectorized environment.
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ADMIX: computing admixture coefficients from molecular data.
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PATHMATRIX:
an extension to the GIS software ArcView 3.x. It computes matrices of
effective distances, based on a least-cost path algorithm.
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MINSPNET: to computes a minimum spanning network among a set of OTUs.
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LAPD: a program to estimate maximum likelihood allele and two-locus haplotype frequencies.
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MismatchHetMutRate: a series of programs to perform mismatch analyses allowing for heterogeneity of mutation rates.
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PGDSpider: powerful automated data conversion tool for population genetic and genomics programs.
Le site de Steven Kalinowski: http://www.montana.edu/kalinowski/Software.htm
Liste des programmes:
HP-Rare
Uses rarefaction to compensate for the effect of sample size on
estimates of the number of alleles and number of private alleles in
samples from hierarchical data.
Null-Freq
Estimates the frequency of null alleles at microsatellite loci.
ML-Relate
Estimates relatedness or relationship among individuals from genetic data.
MM-Dist
Estimates the probability distribution for genetic differences in a
population. This is useful for planning studies using non-invasive DNA
to identify individuals.
HW-QuickCheck
Checks genotypes for agreement with Hardy-Weinberg expectations.
Genotype Viewer
Depicts summary statistics for a GENEPOP file: sample sizes, amount of
missing data, number of alleles, gene frequencies, heterozygosities,
and Fst.
StreamTree
Estimates how much each section of a river contributes to the genetic differentiation among populations.
ONCOR
Software for genetic stock identification (mixture analysis and assignment tests).
TreeFit
Evaluates how well a UPGMA or neighbor-joining tree fits a genetic distance matrix.
Mykiss
Estimates reproductive success and parentage using genetic data.
Sequence Viewer for Students
Educational software for viewing and comparing DNA sequences.
Clarki
Estimates the composition of hybrids using SNP and other diallelic loci that have fixed differences between taxa.
Genetic distances
Calculates common genetic distances from GENEPOP files. These include
Nei's (1987) Ds, Nei's (1987) Da, and Weir and Cockerham's (1984) theta.
GenoQuickSim (for Mark Taper)
Simulates genotypic data using coalescent methods.
Le site de Joe Felsenstein: http://evolution.genetics.washington.edu/phylip/software.html
392 phylogeny packages and 54 free
web servers...