Convert software population genetics download

Mesquite — phylogentics, population genetic, and multivariate analysis. MOE — molecular visualization, modeling, and simulation. MrBayes — Bayesian inference of phylogeny. NeEstimator — estimates effective population size Ne. Network — drawing unrooted networks similar to PopART.

NewHybrids — identification of hybrids. OligoCalc — oligonucleotide properties calculator. OrthoFinder — comparative genomics tool for finding orthogroups, rooted gene trees and species trees, and gene duplication events.

PGDSpider — data conversion tool. PHASE — haplotype reconstruction and recombination rate estimation. Phylogenomics Lab Software — phylogenomics software s e. PhyML — phylogenetic analysis using maximum likelihood for large data sets. PLINK — whole genome association analysis toolset. PopART — unrooted networks similar to Network. Popgenome — population genetics statistics for genomic data sets. Popgen Pipeline Platform — workflow platform for population genomic analyses.

PopLDdecay — linkage disequilibrium decay analysis for variant call format files. Poppr — R package similar to adegenet for analysis of populations with mixed modes of clonal and sexual reproduction.

Pritchard Lab Software — population genetics and other software s e. PSMC — infers population size history from whole-genome diploid consensus sequence.

Rambaut Lab Software — phylogenetics softwares e. Rarefaction Calculator — used for calculating allelic richness standardized to sample size. Relatedness — calculates relatedness. RFMix — models ancestry along an admixed chromosome.

Salmon — quantification of RNA-Seq transcripts. SOAPdenovo — short-read genome assembly. SplitsTree4 — network oriented tool for quantifying tree uncertainty. SnpEff — variant annotation and functional effect prediction. Stacks — RAD-Seq pipeline. Linux: execute the command ". Windows: execute the command "PGDSpider2-cli. Java Web Start provides an easy, one-click activation of PGDSpider and it guarantees that you are always running the latest version.

Have a look at Installation Instructions under 1st step to get information on how to get Java6 RE or a newer version. Formats supported by PGDSpider:. PGDSpider is able to parse 33 and to write 36 different file formats:. Note that, PGDSpider is currently not meant to convert large NGS files as it loads into memory the whole input file, which may lead to memory issues.

However, PGDSpider allows one to convert specific subsets of these NGS files into any other format, and this approach can be used to perform sliding windows analyses on large NGS files.

Help If you have any problems:. Bioinformatics Copyright c , Heidi E. All rights reserved. By using, modifying or distributing this software you agree to be bound by the terms of this license. If there are any bugs, send me an e-mail. Please give me a short description of the bug and tell me the input and output file format. If it is possible also attach the input file which caused the problem. PGDSpider is an on-going project. For any comments or suggestions of further file formats, please send me an e-mail.

Data format. References and Links. External dependency. Input format. Output format. Lischer and Excoffier, Excoffier and Lischer, Li et al. DetSel : Another program that identifies outlier loci by coalescence simulations. Less stringent assumptions than FDist. See alos the publication in the Journal of Heredity.