Research Articles
ASTRAL vs. SVDquartets: A Practical Guide for Species Tree Inference in Genomic Research
This article provides a comprehensive evaluation of two leading coalescent-based species tree estimation methods, ASTRAL and SVDquartets.
Addressing Rate Variation in Phylogenetic Introgression Tests: A Guide for Robust Analysis in Evolutionary and Biomedical Research
This article provides a comprehensive guide for researchers and drug development professionals on the critical issue of substitution rate variation in phylogenetic introgression testing.
Navigating the Gap: A Comprehensive Guide to Handling Missing Data in Phylogenomic Introgression Analysis
Phylogenomic introgression analysis is pivotal for understanding evolutionary histories, yet missing data remains a significant challenge that can bias species tree estimation and introgression detection.
Beyond the False Signal: Strategies to Mitigate Ancestral Polymorphism in Introgression Detection
Accurately identifying true introgression is critical for evolutionary studies and biomedical research, yet it is frequently confounded by false positives from ancestral polymorphism and selection.
Parameter Optimization for Phylogenetic Network Inference: Advanced Methods for Evolutionary Analysis and Biomedical Applications
This article explores cutting-edge parameter optimization techniques transforming phylogenetic network inference, addressing critical computational bottlenecks in analyzing evolutionary relationships.
Optimizing Sequence Alignment Blocks for Accurate Gene Tree Inference: A Practical Guide for Biomedical Researchers
Accurate gene tree inference is foundational for evolutionary studies, drug target discovery, and understanding disease mechanisms, yet it is highly dependent on the quality of input sequence alignments.
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.