Research Articles
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.
A Comprehensive Guide to IQ-TREE: Mastering Maximum Likelihood Gene Tree Estimation for Genomic Research
This guide provides a thorough exploration of IQ-TREE, a powerful software for maximum likelihood phylogenetic analysis.
Adaptive Introgression: The Evolutionary Engine Powering Species Survival in Extreme Environments
This article synthesizes current research on adaptive introgression—the natural transfer of beneficial genetic variants between species—as a critical mechanism for rapid evolution in extreme environments.
Gene Flow: From Genomic Mosaic to Precision Medicine
This article synthesizes the paradigm shift in evolutionary biology from a tree-like to a web-like model of life, driven by the ubiquity of gene flow.
Gene Tree Heterogeneity: Biological Sources, Analytical Challenges, and Implications for Biomedical Research
This article provides a comprehensive overview of the biological processes that generate gene tree heterogeneity, a pervasive phenomenon in phylogenomics where individual gene trees exhibit conflicting evolutionary histories.
Decoding Evolutionary History: A Comprehensive Guide to Detecting Ancient Hybridization from Genomic Data
This article provides a comprehensive resource for researchers and scientists on the detection and analysis of ancient hybridization using genome-scale data.