New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics

PeerJ

article

Alexander Knyshov¹  Eric R.L. Gordon²  Christiane Weirauch¹ 

[1] Department of Entomology, University of California;Department of Ecology and Evolutionary Biology, University of Connecticut

关键词: Phylogenomics;    BLAST;    HMMER;    Orthology;    Alignment;    UCE;    OrthoDB;   

DOI  :  10.7717/peerj.11019

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

200 My) for which annotated genomes exist, and on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated or unannotated, low or high depth shotgun, and target capture assemblies as well or better than other software as assessed by recovering the most genes with maximal coverage and with a low rate of false positives throughout all datasets. When assessing this combination of criteria, ALiBaSeq is frequently the best evaluated tool for gathering the most comprehensive and accurate phylogenetic alignments on all types of data tested. The software (implemented in Python), tutorials, and manual are freely available at https://github.com/AlexKnyshov/alibaseq.

【 授权许可】

CC BY