realSFS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool realSFS
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Tool usage distribution map

This map represents all the scientific publications referring to realSFS per scientific context
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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

 (13)
call_split

Multiple Origin but Single Domestication Led to Oryza sativa

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

[…] hird 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 $RE […]

call_split

Genomics clarifies taxonomic boundaries in a difficult species complex

2017
PLoS One
PMCID: 5726641
PMID: 29232403
DOI: 10.1371/journal.pone.0189417
call_split See protocol

[…] mating 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 (doT […]

library_books

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

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

[…] pulation (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 fo […]

library_books

Genetic variation of world soybean maturity date and geographic distribution of maturity groups

2017
Breed Sci
PMCID: 5515309
PMID: 28744175
DOI: 10.1270/jsbbs.16167

[…] uded sequences similarity, pair-end relationships and sequences quality, all sequence reads were aligned with the reference genome of Williams 82 (). The SNPs of the population were identified by the RealSFS (), and 98,482 SNPs were finally confirmed according to the criteria, from which the SNPs of 371 varieties were polymorphic with a rate of missing and heterozygous alleles calls ≤30% and minor […]

library_books

Fast diffusion of domesticated maize to temperate zones

2017
Sci Rep
PMCID: 5437101
PMID: 28522839
DOI: 10.1038/s41598-017-02125-0

[…] we verified the accuracy of SNP calling in the previous pipeline. Although SNPs generated by the second generation sequencing platforms are error-prone, Fu’s SNP data set was already corrected using realSFS, and the accuracy of SNP calling is high according to multiple validation methods. Secondly, samples with hidden relatedness were removed from the analysis. Thirdly, we removed regions that ha […]

library_books

Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments

2017
PLoS Biol
PMCID: 5388470
PMID: 28399148
DOI: 10.1371/journal.pbio.2001627

[…] hen we estimated population allele frequencies with angsd and used them with the 2D-SFS to compute FST in 10 kb nonoverlapping as well as 10 kb wide, 2 kb step sliding windows across the genome using realSFS from the angsd software package [, ]. As for iHS and H12, we identified the top 0.1% outliers among nonoverlapping windows, based on the genome-wide distribution of π and TD in recombination r […]


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