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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...variants, which constitute the primary data used for inferring cell lineage trees. The primary class of genomic variants studied in this paper is the single nucleotide variant (SNV). We do not consider more complex variants such as copy number variations (CNVs) for cell lineage tree inference (see...
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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
.... The expected average number of intervening crossovers in a generation within (p1, p2) and (p1, p3) are (g2 − g1)/100 and (g3 − g1)/100, respectively.The traditional approach to infer the recombination rates is to use genotype data from a large number of parent–offspring pairs to capture an adequate number...
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Method: Ultrafast genome-wide inference of pairwise coalescence times
- Regev Schweiger and
- Richard Durbin
Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
..., New York. ↵Hejase HA, Mo Z, Campagna L, Siepel A. 2022. A deep-learning approach for inference of selective sweeps from the ancestral recombination graph. Mol Biol Evol 39: msab332. doi:10.1093/molbev/msab332 ↵Hobolth A, Jensen JL. 2014. Markovian approximation to the finite loci coalescent...
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Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
- Bin Zhao,
- John A. Lees,
- Hongjin Wu,
- Chao Yang,
- and Daniel Falush
Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
...PS, Arkin AP. 2010. FastTree 2--approximately maximum-likelihood trees 590 for large alignments. PLoS One 5: e9490. 591 Robinson DF, Foulds LR. 1981. Comparison of phylogenetic trees. Mathematical 592 Biosciences 53: 131-147. 593 Sintchenko V, Holmes EC. 2015. The role of pathogen genomics...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...characterized recombination hotspots and coldspots and investigated potential associations between recombination and genomic features to understand the mechanistic underpinnings and evolutionary consequences of recombination rate variation.Demographic history inferencesThe demographic trajectories, inferred...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...a likelihood for an observed haplotype given an inferred haplotype cluster that resembles calculating genotype likelihoods in WGS data from the trained networks.Variational autoencoderAn autoencoder is a state-of-the-art approach for performing dimensionality reduction by learning a mapping of the space...
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Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
...is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...-scale investigation of recombination rate variation across the equine , as historical recombination rates can be estimated by coalescent analysis of linkage disequilibrium (LD) patterns in high-density SNP data (Auton and McVean 2007). These estimates can help identify putative recombination hotspots and compare...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
...the , as 200 kb was the highest resolution for which pedigree-based recombination rates could be estimated. Population genetic inference was based on genotype likelihoods. ANGSD (Korneliussen et al. 2014)was used to estimate allele frequency likelihoods, obtain a maximum likelihood estimate of the unfolded...
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Method: Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data
- Anand Bhaskar,
- Y.X. Rachel Wang,
- and Yun S. Song
Genome Res. February 2015 25: 268-279; Published in Advance January 6, 2015, doi:10.1101/gr.178756.114
...recombining and evolve independently. Second, Nelson and coworkers used 400 simulated coalescent trees to approximate the likelihood for each combination of demographic parameters, resulting in a noisy likelihood surface. Our method, in contrast, uses exact computation to determine the expected SFS...

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