Purdue University

VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.

To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. This selection of a single effect per variant, is often subjective. So this project is an attempt to make the selection criteria smarter, reproducible, and more configurable. And the default criteria must lean towards best practices.

vcf2phylip is a tool to convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis.

Vcf2tsvpy is a small Python program that converts genomic variant data encoded in VCF format into a tab-separated values (TSV) file.

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Velocyto.py a library for the analysis of RNA velocity.

Velvet is a sequence assembler for very short reads.

VeryFastTree is a highly-tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments.

The Vienna Ab initio Simulation Package VASP is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

Viennarna is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures.

Vim is a highly configurable text editor built to make creating and changing any kind of text very efficient.

The Visualization Toolkit VTK is an open-source, freely available software system for 3D computer graphics, image processing and visualization.

VLC is a free and open source multimedia player for most multimedia formats.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Visual Studio Code

Vsearch is a versatile open source tool for metagenomics.

Wannier90 is an open-source code released under GPLv2 for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of materials with high efficiency and accuracy.

Weblogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

Whatshap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.