Research Articles
Decoding Evolutionary Signals: A Practical Guide to Distinguishing Incomplete Lineage Sorting from Introgression in Phylogenomic Data
Accurately distinguishing between incomplete lineage sorting (ILS) and introgression is a critical challenge in phylogenomics, with profound implications for understanding evolutionary history, species delimitation, and biomedical applications such as drug...
Simulating Introgression under the Coalescent Model with Recombination: A Comprehensive Guide for Evolutionary Genomics
This article provides a comprehensive guide for researchers and scientists on simulating introgression under the coalescent model with recombination, a cornerstone of modern evolutionary genomics.
Optimizing Phylogenetic Analysis: A Comprehensive Guide to Filtering Alignment Blocks for Recombination
This article provides a systematic framework for filtering genomic alignment blocks to mitigate the confounding effects of recombination in phylogenetic analysis.
Beyond the Tree: Integrating Gene Flow into the Multispecies Coalescent Model
The multispecies coalescent (MSC) model provides a powerful framework for inferring species histories from genomic data.
A Comprehensive Guide to Identifying Recombination Breakpoints in Genomic Alignments
This article provides a systematic guide for researchers and bioinformaticians on detecting and analyzing recombination breakpoints within sequence alignments.
PhyloNet: A Comprehensive Guide to Phylogenetic Network Inference for Evolutionary Genomics and Drug Discovery
This article provides a detailed overview of PhyloNet, a powerful software package for inferring phylogenetic networks that represent complex evolutionary histories involving reticulate events like hybridization, horizontal gene transfer, and...
From Genomes to Trees: Advanced Whole-Genome Alignment for Phylogenetic Block Extraction
This article provides a comprehensive guide for researchers and drug development professionals on extracting phylogenetically informative blocks from whole-genome alignments.
Navigating Introgression: A Comprehensive Guide to ASTRAL for Robust Species Tree Estimation
This article provides a comprehensive resource for researchers and bioinformaticians grappling with species tree estimation in the presence of gene flow.
PhyloNet-HMM: A Computational Framework for Detecting Genomic Introgression in Biomedical Research
This article provides a comprehensive overview of PhyloNet-HMM, a powerful computational framework that integrates phylogenetic networks with hidden Markov models to detect introgression—the transfer of genetic material between species—in genomic...
Implementing the ABBA-BABA D-Statistic in Phylogenomics: A Comprehensive Guide from Theory to Practice
This article provides a comprehensive resource for researchers and scientists implementing the ABBA-BABA D-statistic to detect introgression from phylogenomic data.