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Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure

https://doi.org/10.1101/542035

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-4757-2609-1_16openalex-snapshot

An Ancestral Recombination Graph

inferredcites →https://doi.org/10.1016/0040-5809(83)90013-8openalex-snapshot

Properties of a neutral allele model with intragenic recombination

inferredcites →https://doi.org/10.1038/ng.3643openalex-snapshot

A reference panel of 64,976 haplotypes for genotype imputation

inferredcites →https://doi.org/10.1093/bioinformatics/bth097openalex-snapshot

QDist—quartet distance between evolutionary trees

inferredcites →https://doi.org/10.1093/bioinformatics/btu014openalex-snapshot

Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)

inferredcites →https://doi.org/10.1093/bioinformatics/btu861openalex-snapshot

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

inferredcites →https://doi.org/10.1098/rstb.2005.1673openalex-snapshot

Approximating the coalescent with recombination

inferredcites →https://doi.org/10.1101/035170openalex-snapshot

A reference panel of 64,976 haplotypes for genotype imputation

inferredcites →https://doi.org/10.1109/tcbb.2009.27openalex-snapshot

New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations

inferredcites →https://doi.org/10.1109/tcbb.8857openalex-snapshot

IEEE/ACM Transactions on Computational Biology and Bioinformatics

inferredcites →https://doi.org/10.1371/journal.pcbi.1004842openalex-snapshot

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

inferredcites →https://doi.org/10.1371/journal.pgen.1004342openalex-snapshot

Genome-Wide Inference of Ancestral Recombination Graphs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s11047-022-09882-6openalex-snapshot

Computational graph pangenomics: a tutorial on data structures and their applications

inferred← citeshttps://doi.org/10.1038/s41588-019-0483-yopenalex-snapshot

Inferring whole-genome histories in large population datasets

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac734openalex-snapshot

Syllable-PBWT for space-efficient haplotype long-match query

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010409openalex-snapshot

VGsim: Scalable viral genealogy simulator for global pandemic

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008384openalex-snapshot

An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

inferred← citeshttps://doi.org/10.47248/hpgg2606030009openalex-snapshot

TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method

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