VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences

BMC Bioinformatics

Software

Yousef Jaber¹  Omer Gokcumen¹  Duo Xu¹  Pavlos Pavlidis² 

[1] Department of Biological Sciences, State University of New York at Buffalo, 14260, New York, USA;Institute of Molecular Biology and biotechnology (IMBB), Foundation of Research and Technology--Hellas, Heraklion, Crete, Greece;

关键词: VCF;    Phylogeny;    FASTA;    1000Genomes;    Anthropological genetics;    Next generation sequencing data;   

DOI  :  10.1186/s12859-017-1844-0

 received in 2017-05-19, accepted in 2017-09-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundConstructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies.ResultsHere, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format.ConclusionVCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0.

【 授权许可】

CC BY   
© The Author(s). 2017