VISUALIZATION OF CONDENSED MULTIPLE SEQUENCE ALIGNEMENTS AND PHYLOGENETIC TREES

List of participants and affiliations:

• Christian Zmasek (czmasek@jcvi.org) - Team leader
• Chrissy Aceves (caceves@scripps.edu)
• Nate Matteson (natem@scripps.edu)
• Grace Nabakooza (sxv8@cdc.gov)
• Daniel Chen (dchen32@uw.edu)
• Diana Ir (diana.ir@state.co.us)

Table of content

1. Introduction
2. Project goal
3. Prerequisites
4. Installment
5. Input
6. Approach
7. Future work

Introduction

2f6e85ac0acb3f86a87541f91fe8b2340335ea54 Phylogenetic visualization of large multiple sequence alignments is difficult. Since phylogenies are reconstructed based on differences in a multiple sequence alignment (MSA), tools that utilize only the positions with variation in the MSA could improve phylogenetic reconstruction and visualization.

Project goal

We developed a drag and drop interface where the user provides (1) a vcf file and (2) a newick tree file and we render a multiple sequence alignment (MSA) visualization focusing on single nucleotide variants (SNVs).

Prerequisites

• Python 3
• dendropy
• flask
  • Install using python: "https://flask.palletsprojects.com/en/2.1.x/installation/". Flask supports Python 3.7 and newer.
• JavaScript
• Web-Interface

How to use our tool

Installation

1. Download the app.py from "https://github.com/NCBI-Codeathons/beyond-phylogenies-team3/blob/main/app.py" in your current directory
2. The app can be simply run by executing python app.py in the user's command line interface (e.g. Terminal, Command Prompt).

Input

Example VCF and Newick (also called New-Hampshire) file formats are provided in the example-data folder. Upload the files at "http://127.0.0.1:5000/" then click "Visualize Data" and it will render.

Approach

• Create two HTML pages one to submit files and the other to render them
• Create a Flask app to connect Python parsing and webpage output
• Utilize JS to create Drag and Drop system
• Alter React-MSA's underlying code to only show variants of interest
• Alter React-MSA's underlying code to show residue rather than arbitary positions

Future Work

• Summarize nucleotides at reference positions
• Annotate phylogeny with other metadata
• Highlight items on the tree itself
• Real-time calculation of clade-defining substitutions
• Increased options and flexibility in design/algorithms utilized
• Hovering over non-SNPs residue belays reference value