ibdfindr: HMM Toolkit for Inferring IBD Segments from SNP Genotypes
Implements continuous-time hidden Markov models (HMMs) to infer identity-by-descent (IBD) segments shared by two individuals from their single-nucleotide polymorphism (SNP) genotypes. Provides posterior probabilities at each marker (forward-backward algorithm), prediction of IBD segments (Viterbi algorithm), and functions for visualising results. Supports both autosomal data and X-chromosomal data. The current model has two states, non-IBD and IBD1, and is intended for unilineal relationships. The methodology and package are described in Vigeland et al. (2026) <doi:10.1016/j.fsigen.2025.103409>.
| Version: | 0.4.0 |
| Depends: | R (≥ 4.4) |
| Imports: | forrel, ggplot2, ibdsim2, pedtools, ribd |
| Suggests: | testthat (≥ 3.0.0) |
| Published: | 2026-08-31 |
| DOI: | 10.32614/CRAN.package.ibdfindr |
| Author: | Magnus Dehli Vigeland
 [aut, cre] |
| Maintainer: | Magnus Dehli Vigeland <m.d.vigeland at medisin.uio.no> |
| BugReports: | https://github.com/magnusdv/ibdfindr/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/magnusdv/ibdfindr |
| NeedsCompilation: | no |
| Language: | en-GB |
| Citation: | ibdfindr citation info |
| Materials: | README, NEWS |
| CRAN checks: | ibdfindr results |
Documentation:
| Reference manual: | ibdfindr.html , ibdfindr.pdf |
Downloads:
| Package source: | ibdfindr_0.4.0.tar.gz |
| Windows binaries: | r-devel: ibdfindr_0.3.1.zip, r-release: ibdfindr_0.3.1.zip, r-oldrel: ibdfindr_0.3.1.zip |
| macOS binaries: | r-release (arm64): ibdfindr_0.3.1.tgz, r-oldrel (arm64): ibdfindr_0.3.1.tgz, r-release (x86_64): ibdfindr_0.3.1.tgz, r-oldrel (x86_64): ibdfindr_0.3.1.tgz |
| Old sources: | ibdfindr archive |
Reverse dependencies:
| Reverse imports: | pedsuite |
Linking:
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