tutorial.md

FunVIP Tutorial

• Part 1 - Getting started - this page
• Part 2 - Preparing database and query
• Part 3 - How to use FunVIP for final publication

This is basic tutorial for how to run FunVIP In this tutorial, we will run FunVIP with already prepared input files.

Prerequisites

Conda environment should be installed to follow the tutorial

• Conda installation

1. Install FunVIP by following instructions, depending on your os system

• Windows

• Linux

• Mac - Apple Silicon

2. Prepare database and query file

Here, we'll going to use Aspergillus section Terrei dataset from the paper (link will be added after publication)

Download database and query file by clicking

• Database

• Query

If your directory looks like this you are going well

3. Run FunVIP

Turn on your FunVIP conda environment

• conda activate FunVIP

A. Your environment should be "FunVIP"

B. Your current directory should be the place where your database and query file exists

Now you are ready to go. Run FunVIP with single command.

• FunVIP --db FunVIP_Aspergillus_db.xlsx --query FunID_Aspergillus_query.xlsx --email <your email> --gene ITS BenA CaM RPB2 --preset fast --level section

If you see the sign, "FunVIP ended in XXX.Xs", FunVIP has well performed without critical error.

4. See results

Open the result directory. The default result directory will be named by timestamp when you run the program. ex) 20240118-101519

Your result directory will look like this

There are bunch of information here, but we will concentrate on result and phylogenetic trees.

• See <TIMESTAMP>.result.csv file to see overall results

• See ./07_Tree/<TIMESTAMP>_Terrei_concatenated.svg to see phylogenetic tree