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[[Category:Software]][[Category:Biology]][[Category:Variant Calling]] population genetics statistics from large SNPs dataset.

[[Category:Software]][[Category:Biology]][[Category:Genomics]] ...://rajanil.github.io/fastStructure/www.genetics.org/content/197/2/573.full Genetics], [http://rajanil.github.io/fastStructure/biorxiv.org/content/early/2013/12

[[Category:Software]][[Category:Biology]] |{{#vardefine:url|http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html}}

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] Molecular Evolutionary Genetics Analysis

[[Category:Software]][[Category:biology]][[Category:genomics]] ...ing Admixture Histories of Human Populations Using Linkage Disequilibrium. Genetics, 2013.

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...for analysis of genome-wide association studies. American Journal of Human Genetics, 81:1278-1283, 2007]

[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Sequencing]] ...e biology found in many plants and breeding situations.  Compared to human genetics, many crops are highly diverse both at the nucleotide level and structural

[[Category:Software]][[Category:Biology]][[Category:NGS]] ...llele frequency or genetic distances). Besides the conventional population genetics formats, PGDSpider integrates population genomics data formats commonly use

[[Category:Biology]] ...expression quantitative trait loci (eQTL) studies (Zhu et al. 2016 Nature Genetics). The methodology can be interpreted as an analysis to test if the effect s

[[Category:Software]][[Category:Biology]][[Category:Genomics]] ...l method for detecting identity by descent. The American Journal of Human Genetics 88:173-182.

[[Category:Software]][[Category:Genomics]][[Category:Biology]] ...fective population numbers in two populations using a coalescent approach. Genetics, 152(2):763–73, 1999

[[Category:Software]][[Category:Biology]][[Category:Genomics]] ...software for statistical inference in population genetics and evolutionary biology.

[[Category:Software]][[Category:biology]][[Category:NGS]] ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. T

[[Category:Software]][[Category:Biology]][[Category:Genomics]] ...ction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Sequencing]] ...ence of population history from hundreds of unphased whole genomes. Nature Genetics, 49(2):303–309, 2017.]

[[Category:Software]][[Category:genomics‏‎]][[Category:Biology]] ...s Confounding from Polygenicity in Genome-Wide Association Studies. Nature Genetics, 2015.]

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...LFMM computer program includes an integrated framework based on population genetics, ecological modeling and statistical techniques for screening genomes for s

[[Category:Biology, Genetics]]

[[Category:Software]][[Category:Biology]][[Category:Genomics]] ...(2015) Genotype-frequency estimation from high-throughput sequencing data. Genetics (in press).

[[Category:Software]][[Category:Genomics]][[Category:Biology]] ...e using next generation sequence data in samples of arbitrary ploidy. PLoS genetics, 13(1), p.e1006529.

[[Category:Software]][[Category:Biology]][[Category:NGS]] ...ation size from segments of identity by descent. American Journal of Human Genetics. In Press. doi:10.1016/j.ajhg.2015.07.012]

[[Category:Software]][[Category:Phylogenetics]][[Category:Biology]] ...d sample frequency spectrum (SFS), a statistic commonly used in population genetics, and uses it to fit demographic history.

[[Category:Software]][[Category:Biology]][[Category:Genomics]] to the population genetics context.

[[Category:Software]][[Category:Biology]][[Category:imaging]][[Category:Machine Learning]] ...tion of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics...), most often with longitudinal follow-up.

[[Category:Software]][[Category:Genomics]][[Category:Biology]] ...fined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, doi:10.1038/s41588-018-0237-2 (2018).

[[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:url|http://genetics.cs.ucla.edu/metatissue/index.html}}

[[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:url|http://genetics.cs.ucla.edu/egene-mvn/index.html}}

[[Category:Software]][[Category:Biology]][[Category:NGS]] ...ly parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina HiSeq2000 yield unprecedented levels of se

[[Category:Software]][[Category:Biology]][[Category:NGS]] ...imputation in genome-wide association studies through pre-phasing. Nature Genetics 2012.

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...opulation splits and mixtures from genome-wide allele frequency data. PLoS Genetics.]

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...erentiation and Association Analysis with population-specific covariables. Genetics, 201: 1555-1579.]

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...ce et al. (2015). FAST: FAST Analysis of Sequences Toolbox in Frontiers in Genetics, and Stajich et al. (2002)]

[[Category:Software]][[Category:biology]][[Category:genomics]] ...eakthroughs in the accuracy of automated genome annotation. Nature Reviews Genetics, 9(1), 62-73. doi:10.1038/nrg2220

[[Category:Biology]] form. PLOS Genetics 16(11): e1009049

[[Category:Software]][[Category:Phylogenetics]][[Category:Biology]] HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...g Environmental Correlations to Identify Loci Underlying Local Adaptation. Genetics. 2010]

[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] ...e_files/2012_Patterson_AncientAdmixture_Genetics.pdf N. Patterson et al. ''Genetics'', vol 192:'''1065–1093''']

[[Category:Software]][[Category:Biology]][[Category:Genomics]] [3] Hedrick PW. Gametic disequilibrium measures: proceed with caution. Genetics 1987 Oct;117(2):331-41.

[[Category:Software]][[Category:Biology]][[Category:NGS]] ...nd is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme. Platypus has been thoroughly tested on data mapped with Stampy a

[[Category:Software]][[Category:Biology]][[Category:Variant Calling]] ...ropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180: 977-993

[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] Nature Genetics 47, 296-303 (2015)

[[Category:Software]][[Category:Phylogenetics]][[Category:Biology]] .... Foll (2013) Robust demographic inference from genomic and SNP data. PLOS Genetics, 9(10):e1003905.]

[[Category:Software]][[Category:Biology]][[Category:Annotation]] ...studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.