PopGenome protocols

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PopGenome specifications

Information


Unique identifier OMICS_08604
Name PopGenome
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An almost de facto standard for whole-genome variation data is the variant call format (VCF), used, among others, by the 1000 genomes project and the UK10k project. PopGenome can read large SNP data sets stored in this format very efficiently, using indexes created with Tabix.
Input format FASTA, NEXUS, MEGA, MAF, and Phylip
Operating system Unix/Linux
Programming languages C, C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.6.1
Stability Stable
Requirements
methods, parallel, bigmemory, ff, R(≥2.14.2), BASIX, WhopGenome, BlockFeST
Maintained Yes

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Maintainer


  • person_outline Bastian Pfeifer <>

Publication for PopGenome

PopGenome in pipelines

 (8)
2018
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] (π, []) and watterson’s θ (θw), which is based on the number of segregating sites []. for both measurements, synonymous and non-synonymous diversity was calculated separately using the r package popgenome []., 23 m. bovis strains were used for whole genome sequencing, obtained from ten departments of uruguay in the years 1982, 1998, 2005, 2008, 2010, 2014 and 2015. samples […]

2018
PMCID: 5859498
PMID: 29554870
DOI: 10.1186/s12864-018-4604-2

[…] and between u94-u100 genes (fig. ). population genomics analyses including nucleotide diversity estimates, tajima’s d, achaz’s y, and hudson-kaplan recombination estimates were executed using the popgenome r package [, , ]. recombination detection analyses were performed using the dualbrothers package using a window length of 800 bp and a step size of 100 bp []., rna sequencing reads […]

2017
PMCID: 5322909
PMID: 28231283
DOI: 10.1371/journal.pgen.1006546

[…] before a phyml maximum likelihood tree was created using the seaview software []. all trees were visualized using evolview []., fixation index (fst) analysis was performed using the r package popgenome []. for all the 1232 core-genome multiple alignments were converted to vcf format using snp-sites [] and site-wise fst was calculated over all biallelic sites for the subpopulation […]

2017
PMCID: 5383471
PMID: 28405281
DOI: 10.1002/ece3.2782

[…] sympatric population comparisons (allopatric abietinus versus allopatric tristis and sympatric abietinus versus sympatric tristis) using the high‐stringency data set (18,014 snps) and the package popgenome (http://popgenome.weebly.com) in the r environment (pfeifer, wittelsbuerger, ramos‐onsins, & lercher, ). error estimates were generated by jackknife resampling over sets of 50 snps. […]

2017
PMCID: 5389967
PMID: 28450881
DOI: 10.3389/fgene.2017.00044

[…] as the number of private and fixed polymorphisms. we also computed the mean fst between populations for each category of markers. these statistics were calculated using vcftools () and the r package popgenome (). an element was considered as complete if its size was at least 90% of the maximum size for its family. the vcflib script vcffilter was used to split vcfs between complete and truncated […]


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PopGenome in publications

 (43)
PMCID: 5900008
PMID: 29686696
DOI: 10.3389/fgene.2018.00119

[…] was used to detect selection signatures between landrace pigs and yorkshire pigs at each snp in this study. for each snp in a pairwise comparison, the expected fst was calculated with the popgenome v2.2.4 in r ()., a recent selective sweep changes patterns of allele frequency at linked sites, excluding variation at closely linked loci and generating a relative excess of allele […]

PMCID: 5870968
PMID: 29584736
DOI: 10.1371/journal.pone.0194616

[…] that have been impacted by selection in the na1, na2 and na3 populations we calculated several population genetic summary statistics in non-overlapping, 10 kb sliding windows using the r package popgenome []. we chose 10 kb intervals based on patterns of linkage disequilibrium in the f. graminearum genome, which become negligible at distances > 10 kb []. further, pilot analyses exploring […]

PMCID: 5873920
PMID: 29467190
DOI: 10.1534/g3.118.200035

[…] analyses were created using tabix, version 0.2.6 ()., to determine the levels of genetic polymorphism of sialic acid biology genes, we first calculated pairwise nucleotide diversity (π) () using popgenome, version 2.1.6 (). as there may have been variation in when and where human sialic acid biology genes experienced positive selection, we next used four different measures aimed to capture […]

PMCID: 5772174
PMID: 29249661
DOI: 10.1016/j.cub.2017.11.027

[…] tree was reconstructed using raxml v7.3.5 as used during the whole genome tree., we used the software structure v2.3.4 to study the genetic structure of the population []. in addition, we used popgenome to estimate fst between different clades []. we recorded the number of snps in c. glabrata population using the 33 strains. we obtained the number of snp also using 32 different strains […]

PMCID: 5786231
PMID: 29281015
DOI: 10.1093/gbe/evx276

[…] by the authors of the algorithm. a measure of the genetic distance between the three clusters was obtained by computing pairwise nucleotide differences (; ) between and within clusters using the popgenome package in r () and the full snp data., a phylogenetic tree was estimated with the program snphylo (), using the full snp data because ld pruning is performed by the program. brachypodium […]


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PopGenome institution(s)
Institute for Computer Science, Heinrich Heine University, Düsseldorf, Germany; Centre for Research in Agricultural Genomics, Bellaterra, Spain; Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
PopGenome funding source(s)
This work was supported by the Spanish Ministerio de Ciencia e Innovación Grant CGL2009-09346 and by the German Research Foundation DFG grants EXC 1028 and CRC 680.

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