ArticleBiology direct2013
Next-generation phylogenomics.
Article in Biology direct, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Comparative Analysis ofGenes · 2025Article
- PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score.Bioinformatics (Oxford, England) · 2023Article
- Evolutionary History of Sexual Differentiation Mechanism in Insects.Molecular biology and evolution · 2022Article
- In depth search of the Sequence Read Archive database reveals global distribution of the emerging pathogenic fungus Scedosporium aurantiacum.Medical mycology · 2022Article
- Comparative plastomes ofFrontiers in plant science · 2022Article
- Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions.Frontiers in plant science · 2022Article
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- Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution.Scientific reports · 2021Article
- Genomic and evolutionary comparison between SARS-CoV-2 and other human coronaviruses.Journal of virological methods · 2021Article
- A Computational Framework for Pattern Detection on Unaligned Sequences: An Application on SARS-CoV-2 Data.Frontiers in genetics · 2021Article
- Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.Methods in molecular biology (Clifton, N.J.) · 2021Article
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- A systematic comparison of chloroplast genome assembly tools.Genome biology · 2020Article
- Molecular evidence ofParasitology · 2020Article
- Classification of COVID-19 and Other Pathogenic Sequences: A Dinucleotide Frequency and Machine Learning Approach.IEEE access : practical innovations, open solutions · 2020Article
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Efficient merging of genome profile alignments.Bioinformatics (Oxford, England) · 2019Article
- Phylogenetic analysis of Theileria equi and Babesia caballi sequences from thoroughbred mares and foals in Trinidad.Parasitology research · 2019Article
Corrections and comments
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2 authors.
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Abstract
Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. Phylogenomics--the study of evolutionary relationships based on comparative analysis of genome-scale data--has so far been developed as industrial-scale molecular phylogenetics, proceeding in the two classical steps: multiple alignment of homologous sequences, followed by inference of a tree (or multiple trees). However, the algorithms typically employed for these steps scale poorly with number of sequences, such that for an increasing number of problems, high-quality phylogenomic analysis is (or soon will be) computationally infeasible. Moreover, next-generation data are often incomplete and error-prone, and analysis may be further complicated by genome rearrangement, gene fusion and deletion, lateral genetic transfer, and transcript variation. Here we argue that next-generation data require next-generation phylogenomics, including so-called alignment-free approaches.
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