GitHub - bahlolab/isoRelate: Performs pairwise identity by descent analysis on haploid recombining organisms in the presence of multiclonal infections using SNP genotype data (original) (raw)

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. Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens. bioRxiv. doi: http://dx.doi.org/10.1101/088039