Light

jbloomlab / herpesvirus-glycoprotein-analysis Goto Github PK

View Code? Open in Web Editor NEW

0.0 1.0 0.0 897 KB

Analysis of natural diversity in herpesvirus glycoproteins

License: MIT License

Python 99.08% Shell 0.92%

herpesvirus-glycoprotein-analysis's Introduction

Phylogeny analysis for herpesvirus glycoproteins

This repo contains multiple directories that analyze the diversity of specific herpesvirus glycoproteins by running a snakemake pipeline that downloads sequences based a list of accessions, processes the sequences, and constructs a phylogenetic Nextstrain tree that can be viewed using Auspice. Each herpesvirus directory contains its own snakemake pipeline.

Analysis performed by Caleb Carr.

Nextstrain visualizations of the trees

Organization of this repo

HSV1: Contains the analysis workflow for HSV-1
EBV: Contains the analysis workflow for EBV
auspice: Contains the final nextstrain tree files for each herpesvirus that then can be viewed using Nextstrain community share via GitHub. Note that these final files are manually copied from each individual herpesvirus directory.

herpesvirus-glycoprotein-analysis's People

Contributors

Watchers

herpesvirus-glycoprotein-analysis's Issues

Change titles of Nextstrain trees to be more specific

Change the titles of each tree to reflect what is being shown (i.e., what herpesvirus and what glycoprotein is being shown)

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.