Package: sequoia 3.2.0

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]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sequoia/json (API)

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

Bug tracker:https://github.com/jiscah/sequoia/issues

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

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

On CRAN:

Conda:

pedigreepedigree-reconstructionpedigreessequoiasnpsnp-datafortran

7.71 score 29 stars 119 scripts 658 downloads 41 exports 3 dependencies

Last updated from:da0455b273. Checks:11 WARNING, 2 OK. Indexed: yes.

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source / vignettesOK270
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macos-release-arm64WARNING175
macos-release-x86_64WARNING519
macos-oldrel-arm64WARNING189
macos-oldrel-x86_64WARNING451
windows-develWARNING204
windows-releaseWARNING156
windows-oldrelWARNING185
wasm-releaseOK153

Exports:CalcBYprobsCalcMaxMismatchCalcOHLLRCalcPairLLCalcParentProbsCalcRpedCheckGenoComparePairsCountOHDyadCompareErr_RADseqErrToMEstConfFindFamiliesGenoConvertGetAncestorsgetAssignCatGetDescendantsgetGenerationsGetLLRAgeGetMaybeRelGetRelMLHConvertLLtoProbMakeAgePriorMkGenoErrorsPedComparePedPolishPedStripFIDPlotAgePriorPlotPairLLPlotPedCompPlotPropAssignedPlotRelPairsPlotSeqSumsequoiaSimGenoSnpStatsSummarySeqwriteColumnswriteSeq

Dependencies:cliplyrRcpp

Sequoia User Guide
Quick-start examples | Simulated Data | Real Data | Background | Key Points | Mendelian Errors | Parent-pairs | Maximum mismatches | Likelihoods | Genotyping errors | Effect | Assumed genotyping error rate Err | Performance with high genotyping error rates | Effect on runtime | Error matrix | Estimate | Birth years & Ageprior | Definition & interpretation | Implementation | Smooth & Flatten | Age-based non-assignment | Parent LLR | Confidence | Low assignment rate | Causes | Remedies | Function overview | Input | Simulate | Ageprior | Pedigree reconstruction | Pedigree check | Pairwise relationships | Miscellaneous | sequoia() input | Genotypes | Subset SNPs | PLINK | Family IDs | Low call rate | Very large datasets | Birth years & sex | LifeHistData | Unknown birth years | args.AP (Customising the ageprior) | Tfilter & Tassign | Complex | Unusual relationships | Herm | UseAge | SeqList | Running sequoia() | console output | step | dams, sires | Total LL | Module | Input check | Check for duplicates | Parentage assignment | AgePrior | Full reconstruction | Dummy Individuals | Total likelihood | Save output | Output check | Pedigree stats & plots | Negative LLR's | Dyad plot | Likely relatives | Compare pedigrees | Dummy matching | Example | Colony | Relatedness | Pedigree relatedness | Genomic relatedness | Cluster families | Hermaphrodites | Herm 'A': Pedigree prior | Herm 'B': Ignore sex role | Hermaphrodite dummies | Duplicate check | Assignment errors | Parthenogenesis | FAQ | Error about/due to input data | Low assignment rate | Not enough SNPs | Too many SNPs | Genotyping errors | Lacking sex information | Insufficient age information | Uninformative age prior | Mating system | Death year | Accuracy | Field pedigree | Data simulation | Add new individuals | Results differ from COLONY | References
Rendered fromvignette-main.Rmdusingknitr::rmarkdown

Last update: 2025-08-10
Started: 2021-03-26

Sequoia - Age 'Prior'
In short | Age Info is Useful | Implementation | Passing the threshold | Time units | Runtime Messages | Changing the ageprior | Maths | AgePrior | Unsampled individuals | Genetics $\times$ Age | AgePrior matrix explained | AgePriorExtra | Default ageprior | Pedigree-based ageprior | Discrete generations | Generation interval different from 1 | Overlapping generations | BirthYearRange | MaxAgeParent | Counts: tblA.R | P(A|R): PA.R | Full sibling correction | Ageprior P(A|R)/P(A): LR.RU.A.raw | Small sample correction | The problem | Smooth | Flatten | Weighing factor & lambdaNW | Sample size vs. sampling probability | Grandparents & Avuncular | Ageprior to Probability to Ageprior | change from v1.3 to v2.0 | Customise | Via args.AP | Different input pedigree | Other tweaks | From age-difference distribution | Specifications | Estimate birth years | References
Rendered fromvignette-age.Rmdusingknitr::rmarkdown

Last update: 2025-07-16
Started: 2021-03-26

Mitochondrial haplotypes
Why use mitochondrial data | Limitations | Input | Example
Rendered fromvignette_mtDNA.pdf.asisusingR.rsp::asis

Last update: 2023-12-14
Started: 2023-12-14

Quick start example 1: Simulated data
Get started | Simulate genotypes | Parentage assignment | Pedigree reconstruction | Save results
Rendered fromquick_start_example1.rmdusingknitr::rmarkdown

Last update: 2023-01-20
Started: 2021-03-26

PedCompare Example (Griffin Pedigree)
Example: PedCompare | Why compare pedigrees | Study population | Comparing pedigrees | $MergedPed | id columns | $DummyMatch | $Counts | Mismatch | Mismatch Issue1: GreenBlue | Mismatch Issue2: OrangeGreen | Mismatch Issue3: YellowBlue | Mismatch Issue4: GreenYellow | Pedigree1-only | General | Griffins | Pedigree2-only (newly assigned mum) | Warning re dummy numbering
Rendered fromPedComp.Rmdusingknitr::rmarkdown

Last update: 2023-01-10
Started: 2021-03-26

Sequoia flowchart
Rendered fromflowchart.pdf.asisusingR.rsp::asis

Last update: 2021-04-29
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
Estimate genotyping error rate (REMOVED; will be re-implemented)EstEr
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