TY - JOUR AU - Chan, Cheong Xin AU - Ragan, Mark A. PY - 2013 DA - 2013/01/22 TI - Next-generation phylogenomics JO - Biology Direct SP - 3 VL - 8 IS - 1 AB - 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. SN - 1745-6150 UR - https://doi.org/10.1186/1745-6150-8-3 DO - 10.1186/1745-6150-8-3 ID - Chan2013 ER -