pcadapt protocols

View pcadapt computational protocol

pcadapt statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Unclassified tools chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

pcadapt specifications

Information


Unique identifier OMICS_27301
Name pcadapt
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Michael Blum <>

Publication for pcadapt

pcadapt in pipeline

2018
PMCID: 5859105
PMID: 29593776
DOI: 10.3389/fgene.2018.00068

[…] (guillot et al., ), structure (pritchard et al., ), tess (durand et al., ), popgraph (dyer and nason, ); bayescan foll and gaggiotti, , flk (bonhomme et al., ), bayenv2 (günther and coop, ), pcadapt (duforet-frebourg et al., ) faststructure (raj et al., ), admixture (alexander et al., ), tess3 (caye et al., )., indicates methods not yet widely used but show promise–see sections […]


To access a full list of citations, you will need to upgrade to our premium service.

pcadapt in publications

 (14)
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] populations were included in the outlier detection analyses. bayescan analyses identified 98 outlier loci within the limpet populations, all of which identified as under diversifying selection. pcadapt [] selected a larger amount of outlier loci compared to bayescan, with a total of 355 outliers. only 34 outlier snps were detected by both bayescan and pcadapt, and the number of outliers […]

PMCID: 5870821
PMID: 29580201
DOI: 10.1186/s12864-018-4579-z

[…] we used a population differentiation (pd) method, which investigates the existence of highly differentiated snps across the genome without assuming the effect of a particular environmental variable. pcadapt estimates population differentiation at each snp and compares the value with an expected estimation, calculated from the genome wide background. the null assumption tested is that each snp […]

PMCID: 5859105
PMID: 29593776
DOI: 10.3389/fgene.2018.00068

[…] (guillot et al., ), structure (pritchard et al., ), tess (durand et al., ), popgraph (dyer and nason, ); bayescan foll and gaggiotti, , flk (bonhomme et al., ), bayenv2 (günther and coop, ), pcadapt (duforet-frebourg et al., ) faststructure (raj et al., ), admixture (alexander et al., ), tess3 (caye et al., )., indicates methods not yet widely used but show promise–see sections […]

PMCID: 5919736
PMID: 29255116
DOI: 10.1534/g3.117.300099

[…] to distinguish these candidates of selection, we followed the methodology of to identify markers excessively related to population structure in our experiment. using our frequency estimates and the pcadapt software (), we generated sequencing read counts for every marker for 250 tetraploid individuals from the 12 pooled samples using the read.pcadapt function under pool-seq mode. these data […]

PMCID: 5693503
PMID: 29149838
DOI: 10.1186/s12863-017-0557-8

[…] pgdspider v. 2.1.0.0 [] was used to convert data to genepop format before bayescan v2.1. [] was run under default settings. outlier snps found to be under selection were independently verified using pcadapt, where principle components (k), ranging from 1 to 15 were initially compared using a “scree plot”. a value of k = 10 and a stringent false discovery rate (alpha = 0.001) were implemented […]


To access a full list of publications, you will need to upgrade to our premium service.

pcadapt institution(s)
Université Grenoble Alpes, CNRS, Laboratoire TIMC-IMAG, UMR 5525, France; Université Grenoble Alpes, CNRS, Laboratoire d’Ecologie Alpine UMR 5553, France
pcadapt funding source(s)
Supported by the LabEx PERSYVAL-Lab (ANR-11-LABX-0025- 373 01) and the ANR AGRHUM project (ANR-14-CE02-0003-01).

pcadapt reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review pcadapt