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Arlequin
A software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans.
GenAlEx / Genetic Analysis in Excel
A cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included.
pegas / Population and Evolutionary Genetics Analysis System
A package for the analysis of population genetic data. pegas provides functions for standard population genetic methods, as well as low-level functions for developing new methods. The flexible and efficient graphical capabilities of R are used for plotting haplotype networks as well as for other functionalities. pegas emphasizes the need to further develop an integrated-modular approach for software dedicated to the analysis of population genetic data.
PopGenome
A population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess statistical significance based on coalescent simulations. PopGenome's integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics.
PopART / Population Analysis with Reticulate Trees
Allows population genetics analysis using haplotype networks. PopART primary function is the inference and visualization of genetic relationships among intraspecific sequences. The software includes implementations of minimum spanning, median-joining and TCS network methods and provides a framework for the implementation and distribution of new methods. It also provides basic statistics that are useful for population genetics analyses, as well as tools for visualizing the geographical distribution of genetic data using a map-based interface.
PGEToolbox
A powerful and flexible Matlab toolbox dedicated to the analysis of DNA sequence polymorphisms and SNPs. The main features of PGEToolbox are as follows: 1) capability for handling both DNA sequence polymorphisms and single nucleotide polymorphisms (SNPs), which include genotype and haplotype data; 2) exhaustive population genetic analyses and neutrality tests based on the coalescent theory; 3) extendibility and scalability for complex and large genome-wide datasets; 4) simple yet effective graphic user interfaces and sophisticated visualization of data and results.
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