Usage Guide

Usage Guide for the PHYLOViZ Web Platform

Welcome to the Usage Guide for the PHYLOViZ Web Platform! This guide will provide you with detailed instructions on how to effectively utilize the platform's features for data analysis, visualization, and advanced tools. Whether you're a beginner or an experienced user, this guide will help you make the most of the platform's capabilities.

Table of Contents

1. Managing Projects
2. Uploading Files
3. Managing Datasets
4. Performing Phylogenetic Analysis
5. Visualizing Phylogenetic Data

Managing Projects

To get started with your analysis, you need to create a project. A project serves as a container for your datasets, analyses, and visualizations. Follow these steps to create a new project:

1. From the homepage or the navigation bar, click on "New Project";

2. Fill in the project details, such as the name and description;
3. Click "Create" to create your project.

Upon creating a project, you will be redirected to the project page, where you can begin uploading files, creating your datasets and performing your phylogenetic analysis tasks. This page serves as the central hub for managing and organizing your project-specific data and analyses.

You can access the project and any existing projects by clicking on the "Open Project" button.

This button will redirect you to the list of available projects. From there, you can select and open the desired project to access its respective project page.

Uploading Files

With your project open, you can navigate to the "Upload Files" section to upload files from your local machine to the project. Follow these steps to upload files:

1. Navigate to the "Upload Files" page;
2. Select and upload your data files.

Once the upload is complete, the files will appear in the project structure and can be included in datasets.

Managing Datasets

After uploading your files, you can create datasets for analysis. Follow these steps to create a dataset:

1. Navigate to the "Create Dataset" page.
2. Fill in the dataset details, such as the name and description;
3. Choose the files to include in the dataset;
4. Click "Finish" to create your dataset.

With your dataset created, you can proceed to perform phylogenetic analysis tasks.

Performing Phylogenetic Analysis

The PHYLOViZ Web Platform provides a comprehensive set of powerful tools for performing phylogenetic analysis on your datasets. These tools allow you to gain insights into the evolutionary relationships and genetic diversity within your data. Here are some key operations available for dataset analysis:

• Compute Distance Matrices: Calculate genetic distances between sequences or samples in your dataset. Distance matrices provide valuable information for constructing phylogenetic trees and analyzing genetic relatedness.

• Compute Phylogenetic Trees: Construct phylogenetic trees based on the genetic relationships inferred from your dataset. Phylogenetic trees visualize the evolutionary branching patterns and help identify ancestral relationships among the sequences.

• Compute Tree Views: Generate different views of the constructed phylogenetic trees to analyze and interpret the evolutionary relationships. This includes exploring different tree layouts, branch support values, and tree annotation options.

These operations can be accessed and performed within the available options for your dataset. By utilizing these tools, you can gain a deeper understanding of the genetic relationships and evolutionary history present in your data.

Please note that the specific operations and tools available may vary depending on the nature of your dataset and the features provided by the platform. Refer to the platform's documentation or consult the support team for detailed instructions on how to perform specific phylogenetic analysis tasks.

When you initiate a computation, a corresponding workflow is activated. To track the progress of this workflow, you can conveniently access the "Workflows" section within the project structure, where you'll find the current status of the workflow.

Next, let's explore how you can visualize your data to gain further insights and interpretations.

Visualizing Phylogenetic Data

In addition to performing phylogenetic analysis, the PHYLOViZ Web Platform offers robust visualization capabilities to explore and interpret your data. You can visualize various aspects of your phylogenetic data, including:

• Typing Data: Visualize the genetic typing information associated with your samples, such as allele profiles or sequence types.

• Isolate Data: Explore individual isolates or samples within your dataset and visualize their attributes, such as metadata or genetic characteristics. This enables a detailed examination of specific samples and their relationships.

• Distance Matrices: Visualize distance matrices, which represent the genetic distances between pairs of samples in your dataset. Distance matrices provide a comprehensive overview of the genetic relatedness and diversity within your data.

• Phylogenetic Trees: Visualize the constructed phylogenetic trees that represent the evolutionary relationships among the samples. Phylogenetic trees enable the identification of ancestral relationships and the exploration of branching patterns. Customize the visualization of phylogenetic trees by applying various transformations. You can adjust the layout, modify branch support values, and annotate the tree with additional information. This flexibility allows for the customization and tailored exploration of the phylogenetic tree visualization.

To further enhance your data exploration, the platform provides features such as search, filtering, and sorting. These tools enable you to navigate and analyze your data effectively, focusing on specific subsets or attributes of interest. By leveraging these features, you can uncover hidden patterns, identify outliers, and gain deeper insights into your phylogenetic data.

Whether you are examining genetic relationships, analyzing population structures, or investigating transmission patterns, the visualization capabilities of the PHYLOViZ Web Platform empower you to explore and understand your data in a comprehensive and customizable manner.

Conclusion

Congratulations! You have now familiarized yourself with the usage guide for the PHYLOViZ Web Platform. By following the steps and utilizing the various features discussed in this guide, you can effectively manage projects, upload files, create datasets, perform phylogenetic analysis, visualize and explore data.

If you encounter any difficulties or have further questions, don't hesitate to consult the platform's documentation or reach out to our support team for assistance.

Happy analyzing and visualizing with the PHYLOViZ Web Platform!