Phylogenomic approaches to detecting and characterizing introgression

MS Hibbins, MW Hahn - Genetics, 2022 - academic.oup.com
Phylogenomics has revealed the remarkable frequency with which introgression occurs
across the tree of life. These discoveries have been enabled by the rapid growth of methods …

A general and efficient representation of ancestral recombination graphs

Y Wong, A Ignatieva, J Koskela, G Gorjanc… - Genetics, 2024 - academic.oup.com
As a result of recombination, adjacent nucleotides can have different paths of genetic
inheritance and therefore the genealogical trees for a sample of DNA sequences vary along …

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

E Paradis, K Schliep - Bioinformatics, 2019 - academic.oup.com
After more than fifteen years of existence, the R package ape has continuously grown its
contents, and has been used by a growing community of users. The release of version 5.0 …

Inferring whole-genome histories in large population datasets

J Kelleher, Y Wong, AW Wohns, C Fadil, PK Albers… - Nature …, 2019 - nature.com
Inferring the full genealogical history of a set of DNA sequences is a core problem in
evolutionary biology, because this history encodes information about the events and forces …

Efficient coalescent simulation and genealogical analysis for large sample sizes

J Kelleher, AM Etheridge… - PLoS computational …, 2016 - journals.plos.org
A central challenge in the analysis of genetic variation is to provide realistic genome
simulation across millions of samples. Present day coalescent simulations do not scale well …

PhyloNetworks: a package for phylogenetic networks

C Solís-Lemus, P Bastide, C Ané - Molecular biology and …, 2017 - academic.oup.com
PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of
phylogenetic networks in an interactive environment. Inference of phylogenetic networks is …

[图书][B] Alignment of biological sequences with Jalview

JB Procter, GM Carstairs, B Soares, K Mourão… - 2021 - Springer
In this chapter, we introduce core functionality of the Jalview interactive platform for the
creation, analysis, and publication of multiple sequence alignments. A workflow is described …

Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks

DH Huson, C Scornavacca - Systematic biology, 2012 - academic.oup.com
Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It
provides a number of methods for drawing and comparing rooted phylogenetic networks …

A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis

T Flouri, X Jiao, B Rannala… - Molecular biology and …, 2020 - academic.oup.com
Recent analyses suggest that cross-species gene flow or introgression is common in nature,
especially during species divergences. Genomic sequence data can be used to infer …

Bayesian inference of species networks from multilocus sequence data

C Zhang, HA Ogilvie, AJ Drummond… - Molecular biology and …, 2018 - academic.oup.com
Reticulate species evolution, such as hybridization or introgression, is relatively common in
nature. In the presence of reticulation, species relationships can be captured by a rooted …