/isoRelate

Performs pairwise identity by descent analysis on haploid recombining organisms in the presence of multiclonal infections using SNP genotype data

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DOI

isoRelate: software for inferring pairwise identity by descent in haploid species

Features

  • Estimates the proportion of genome shared IBD between pairs of isolates
  • Detects genomic regions that are identical by descent (IBD) between pairs of isolates
  • Allows IBD detection in isolates with multiple infections
  • Identifies genomic loci under positive selection
  • Creates networks of related isolates
  • Includes multiple graphical functions to explore the results

How to install isoRelate

isoRelate is currently available to install as a development version from Github:

# first install the devtools package
install.packages("devtools")

# install isoRelate using devtools packages
devtools::install_github("bahlolab/isoRelate")

How to use isoRelate

See the introduction vignette for details.

Reference

Henden L, Lee S, Mueller I, Barry A, Bahlo M. 2016. Detecting selection signals in Plasmodium falciparum using identity-by-descent analysis. bioRxiv. doi: http://dx.doi.org/10.1101/088039