realSFS statistics

info info

Citations per year

info

Popular tool citations

chevron_left SNP detection chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

realSFS specifications

Information


Unique identifier OMICS_00071
Name realSFS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://128.32.118.212/thorfinn/realSFS/realSFS.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Thorfinn Sand Korneliussen <>

realSFS citations

 (20)
library_books

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

2018
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] rna-seq reads (aligned using bowtie2 v. 2.2.3 to our evigene-enriched reference transcriptome), restricting analyses to the coding sequence of each transcript. first, we used the angsd dosaf and realsfs commands to calculate genotype likelihoods and the folded site frequency spectrum from the bam files. second, we used this site frequency spectrum as prior to calculate diversity measures […]

library_books

Multiple Origin but Single Domestication Led to Oryza sativa

2018
PMCID: 5844301
PMID: 29301862
DOI: 10.1534/g3.117.300334

[…] of the number individuals in the subpopulation, while –setmaxdepth was set as five times the number individuals in the subpopulation. overall site frequency spectrum was then calculated with the realsfs program from the angsd package. using each subpopulation’s site frequency spectrum as prior, we then calculated θ for each subpopulation using angsd with the command:, angsd –b $bamlist –ref […]

library_books

Genomics clarifies taxonomic boundaries in a difficult species complex

2017
PMCID: 5726641
PMID: 29232403
DOI: 10.1371/journal.pone.0189417

[…] a site frequency spectrum (sfs) for each population (dosaf; []) using paired-end bam files. two-dimensional sfs and global fst (weighted) between each population pair were then estimated using realsfs []., to calculate watterson’s theta [] and tajima’s theta [], sfs estimated as described above were used as priors (pest) with paired-end bam files to calculate each statistic for each site […]

library_books

QTL mapping using an ultra high density SNP map reveals a major locus for grain yield in an elite rice restorer R998

2017
PMCID: 5589899
PMID: 28883457
DOI: 10.1038/s41598-017-10666-7

[…] irgsp 1.0 (http://rapdb.dna.affrc.go.jp/) using soapaligner program. consensus sequences for each individual were generated by soapsnp. input file was prepared by samtools for snp calling with realsfs. population snp calling was performed with realsfs, based on the bayesian estimation of site frequency at each site. the likelihoods of genotypes for each individual were integrated and sites […]

library_books

The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

2017
PMCID: 5559211
PMID: 28835916
DOI: 10.1126/sciadv.1603198

[…] (dosaf) () using paired-end bam files for steelhead and single-end bam files for chinook. two-dimensional sfs and global fst (weighted) between each population pair were then estimated using realsfs ()., to calculate watterson’s θ (), tajima’s θ (), and tajima’s d (), we used sfs that were estimated as described above as priors (pest) with paired-end bam files to calculate each statistic […]

library_books

Construction of high density genetic map and QTL mapping of yield related and two quality traits in soybean RILs population by RAD sequencing

2017
PMCID: 5477377
PMID: 28629322
DOI: 10.1186/s12864-017-3854-8

[…] conducted at the beijing genome institute (bgi) tech, shenzhen, china. the soybean reference genome from williams 82 was used for read mapping with soap software []. input data for snp calling with realsfs was prepared by samtools []. according to site frequency at every site, population snp calling was performed with realsfs. the likelihoods of genotypes for each individual were integrated […]


Want to access the full list of citations?

realSFS reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review realSFS