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FinePop

Fine-Scale Population Analysis

Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.

Functions (16)

Jost's D

EBDJ

Empirical Bayes estimator of Jost's D

Empirical Bayes estimator of Fst.

Empirical Bayes estimator of Hedrick's G'st

FinePop-package

Fine-Scale Population Analysis

Bootstrap sampler of Fst

Regression analysis of environmental factors on genetic differentiation

GstH

Hedrick's G'st

GstN

Nei's Gst.

Nei and Chesser's Gst

clip.genepop

Remove designated markers from a GENEPOP file.

An example dataset of Atlantic herring.

An example dataset of Japanese Spanich mackerel in GENEPOP and frequency format.

read.frequency

Create an allele (haplotype) frequency data object of populations from a frequency format file.

read.genepop

Create a genotype data object of populations from a GENEPOP format file.

thetaWC.pair

Weir and Cockerham's theta adapted for pairwise Fst.

FinePop

Fine-Scale Population Analysis

v1.5.1

GPL (>= 2.0)

Authors

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

Initial release

2018-10-25

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