HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees:

Evolutionary Bioinformatics

Tomáš Fér¹ 

关键词: Target enrichment;    phylogenomics;    genome skimming;    species tree;    locus selection;   

DOI  :  10.1177/1176934317742613

学科分类：生物技术

来源: Sage Journals

【 摘 要 】

Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of “quality-filtered” genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes.

【 授权许可】

Unknown