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PGEToolbox specifications

Information


Unique identifier OMICS_11079
Name PGEToolbox
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Version 3.0
Stability Stable
Requirements
MBEToolbox
Maintained Yes

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Maintainer


  • person_outline James Cai <>

Publication for PGEToolbox

PGEToolbox in publications

 (8)
PMCID: 4517385
PMID: 26215102
DOI: 10.1186/s12864-015-1761-4

[…] q. garryana. h is expected to be negative when there is positive selection leading to high frequency of a derived allele. to calculate h, we used c++ code equivalent to faywu00h_test in the matlab pgetoolbox [], and as the ancestral sequence, we used the q. garryana allele, or, when missing, the most common allele across the q. lobata individuals. the latter choice should bias the h estimates […]

PMCID: 4164438
PMID: 25222615
DOI: 10.1371/journal.pone.0105410

[…] and japanese from tokyo [jpt]) populations. the population genetic differentiation statistic fst among hapmap ii populations (i.e., ceu, asn, and yri [yoruba from ibadan]) was computed using the pgetoolbox and spsmart , . putative positive snps (i.e., those in the top 10%) were further analyzed using pairwise population comparisons. the use of fst is advantageous given that fst measures […]

PMCID: 3939361
PMID: 24464101
DOI: 10.1038/ng.2878

[…] bound of the number of clusters varying over the interval 50-300 across the runs., to estimate the nucleotide diversity π for the euroamerican and beijing clades, the functions available in the pgetoolbox were used in parallel on a cluster computing environment. the very large number of sequences in each clade would require excessive amounts of computing resources when analyzing […]

PMCID: 3381677
PMID: 22534164
DOI: 10.1093/gbe/evs043

[…] is much more frequent than mutation in h. pylori (; ; ), which makes the four-gamete test method suitable for the estimation of recombination events. we used the method implemented in the pgetoolbox (), which filters gaps in advance. we used the minimum number of recombination events divided by gene length in nucleotides (rmin/nt) as a measure of recombination rate., we identified […]

PMCID: 3310733
PMID: 22457636
DOI: 10.1371/journal.pgen.1002578

[…] due to hitchhiking with some other functional variants on this gene, we analyzed all the known hapmap snps on tyrp1 in yri and ceu, and computed their linkage disequilibrium (ld) r2 with rs683 using pgetoolbox (figuere s8). we also considered snps in the 5-kb upstream region of tyrp1. most snps that showed significant ld with rs683 are intronic and do not overlap with any annotated splice […]


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PGEToolbox institution(s)
Department of Biology, Stanford University, Stanford, CA, USA

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