VCFtoTree
VCFtoTree is a software tool for constructing locus-specific phylogenies and sequence alignments. The VCFtoTree pipeline can download genome variation data from online public databases, such as 1000 Genomes Project, and includes tree building and sequence alignment algorithms.
Topic
Phylogenetics;Genomics;Sequence analysis;Population genetics
Detail
Operation: Phylogenetic tree generation
Software interface: Graphical user interface
Language: Python
License: -
Cost: Free
Version name: 3.0.0
Credit: UB Research Foundation through IMPACT grant program.
Input: fa.gz, vcf.gz
Output: FASTA, Newick
Contact: Duo Xu duoxu@buffalo.edu, Omer Gokcumen omergokc at buffalo.edu, Izzy Starr istarr at buffalo.edu
Collection: -
Maturity: -
Publications
- VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.
- Xu D, Jaber Y, Pavlidis P, Gokcumen O. VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. BMC Bioinformatics. 2017 Sep 26;18(1):426. doi: 10.1186/s12859-017-1844-0. PMID: 28950836; PMCID: PMC5615795.
- https://doi.org/10.1186/s12859-017-1844-0
- PMID: 28950836
- PMC: PMC5615795
Download and documentation
Documentation: https://github.com/duoduoo/VCFtoTree_3.0.0/blob/master/VCFtoTreeManual_V3.0.0_Oct.pdf
Home page: https://github.com/duoduoo/VCFtoTree_3.0.0
Links: https://www.dropbox.com/sh/sewjxmh9207fp89/AAASfUGqMBtd2_HO3CR7XA3ha?dl=0
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