Package: sequoia 3.2.0

Jisca Huisman

sequoia: Pedigree Inference from SNPs

Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<doi:10.1111/1755-0998.12665>) for more information.

Authors:Jisca Huisman [aut, cre]

sequoia_3.2.0.tar.gz
sequoia_3.2.0.tar.gz(r-4.7-arm64)sequoia_3.2.0.tar.gz(r-4.7-x86_64)sequoia_3.2.0.tar.gz(r-4.6-arm64)sequoia_3.2.0.tar.gz(r-4.6-x86_64)
sequoia_3.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
sequoia/json (API)
NEWS

# Install 'sequoia' in R:
install.packages('sequoia', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Pkgdown/docs site:https://jiscah.github.io

Uses libs:
  • fortran– Runtime library for GNU Fortran applications
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

fortran

4.46 score 1 stars 159 scripts 687 downloads 41 exports 3 dependencies

Last updated from:045c4fde57. Checks:4 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING192
linux-devel-x86_64WARNING179
source / vignettesOK279
linux-release-arm64WARNING165
linux-release-x86_64WARNING161
wasm-releaseOK158

Exports:CalcBYprobsCalcMaxMismatchCalcOHLLRCalcPairLLCalcParentProbsCalcRpedCheckGenoComparePairsCountOHDyadCompareErr_RADseqErrToMEstConfFindFamiliesGenoConvertGetAncestorsgetAssignCatGetDescendantsgetGenerationsGetLLRAgeGetMaybeRelGetRelMLHConvertLLtoProbMakeAgePriorMkGenoErrorsPedComparePedPolishPedStripFIDPlotAgePriorPlotPairLLPlotPedCompPlotPropAssignedPlotRelPairsPlotSeqSumsequoiaSimGenoSnpStatsSummarySeqwriteColumnswriteSeq

Dependencies:cliplyrRcpp

Mitochondrial haplotypes

Rendered fromvignette_mtDNA.pdf.asisusingR.rsp::asison Jun 08 2026.

Last update: 2024-05-28
Started: 2023-09-06

PedCompare Example (Griffin Pedigree)

Jisca Huisman ( jisca.huisman @ gmail.com )

Rendered fromPedComp.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2024-05-28
Started: 2021-04-29

Quick start example 1: Simulated data

J Huisman

Rendered fromquick_start_example1.rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2024-05-28
Started: 2021-04-29

Sequoia - Age 'Prior'

Jisca Huisman

Rendered fromvignette-age.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-08-19
Started: 2021-04-29

Sequoia flowchart

Rendered fromflowchart.pdf.asisusingR.rsp::asison Jun 08 2026.

Last update: 2024-05-28
Started: 2021-04-29

Sequoia User Guide

Jisca Huisman ( jisca.huisman @ gmail.com )

Rendered fromvignette-main.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-08-19
Started: 2021-04-29

Readme and manuals

Help Manual

Help pageTopics
Birth year probabilitiesCalcBYprobs
Maximum Number of MismatchesCalcMaxMismatch
Calculate OH and LLR for a pedigreeCalcOHLLR
Calculate Likelihoods for Alternative RelationshipsCalcPairLL
Calculate assignment probabilitiesCalcParentProbs
Calculate Pedigree RelatednessCalcRped
Check Genotype MatrixCheckGeno
Compare Pairwise RelationshipsComparePairs
Example output from estimating confidence probabilities: griffinsConf_griffin
Count opposing homozygous SNPs between pairs of individualsCountOH
Compare Dyads (DEPRECATED)DyadCompare
Convert Genotyping Error Rates from per-allele to per-locusErr_RADseq
Generate Genotyping Error MatrixErrToM
Confidence ProbabilitiesEstConf
Example field-observed mothers: griffinsFieldMums_griffin
Assign Family IDsFindFamilies
Example genotype file: GriffinsGeno_griffin
Example genotype file: 'HSg5'Geno_HSg5
Convert Genotype DataGenoConvert
Get ancestorsGetAncestors
Assignability of Reference PedigreegetAssignCat
Get descendantsGetDescendants
Count GenerationsgetGenerations
LLR-age from Ageprior MatrixGetLLRAge
Find Putative RelativesGetMaybeRel
Matrix with Pairwise RelationshipsGetRelM
Inheritance patternsInherit_patterns
Example life history data: griffinsLH_griffin
Example life history file: 'HSg5'LH_HSg5
Extract Sex and Birth Year from PLINK FileLHConvert
transform log-likelihoods to probabilitiesLLtoProb
Age PriorsMakeAgePrior
Example output from check for relatives: griffinsMaybeRel_griffin
Simulate Genotyping ErrorsMkGenoErrors
Example pedigree: griffinsPed_griffin
Example pedigree: 'HSg5'Ped_HSg5
Compare Two PedigreesPedCompare
Fix PedigreePedPolish
Back-transform IDsPedStripFID
Plot Age PriorsPlotAgePrior
Plot Pair Log10-LikelihoodsPlotPairLL
Visualise PedCompare OutputPlotPedComp
Plot proportion of individuals that has a parent assignedPlotPropAssigned
Plot Pairwise RelationshipsPlotRelPairs
Plot Summary Overview of sequoia OutputPlotSeqSum
Example output from pedigree inference: griffinsSeqOUT_griffin
Example output from pedigree inference: 'HSg5'SeqOUT_HSg5
Pedigree Reconstructionsequoia
Simulate GenotypesSimGeno
Example genotype file: 'HSg5'SimGeno_example
SNP Summary StatisticsSnpStats
Summarise Sequoia Output or PedigreeSummarySeq
Write Data to a File Column-wisewriteColumns
Write Sequoia Output to FilewriteSeq