inst/shinyWGD/www/content/introduction.md

In shinyWGD: 'Shiny' Application for Whole Genome Duplication Analysis

shinyWGD

Welcome to shinyWGD Server – a freely accessible and inclusive platform, providing an open space for users to explore and analyze Whole Genome Duplication (WGD) events.

Designed with a user-friendly interface, shinyWGD empowers users with an intuitive, interactive platform that eliminates the need for programming skills. Whether you're a experienced researcher or new to WGD analysis, shinyWGD offers a comprehensive solution.

Our server comprises two key components. First, we've streamlined the process of preparing essential inputs for existing packages, providing an interactive experience for users. Second, shinyWGD offers a meticulously crafted environment for exploring and visualizing WGD events, ensuring a smooth and insightful analysis.

Dive into the world of WGD analysis with shinyWGD Server – freely distributed and tailored to meet your genomic exploration needs.

The structure of shinyWGD

• Home

• Scripts

• Data Preparation
  • This module effortlessly readies inputs for a selection of integrated packages, including wgd, ksrates, i-ADHoRe and OrthoFinder. With a fixed number of studied species, this module automatically generates the necessary inputs for each package, simplifying your workflow and enhancing the efficiency of your genomic analyses.
• Whale Preparation
  • This module seamlessly integrates the powerful capabilities of the Whale package, enabling the inference of reconciled gene trees and model parameters for gene family evolution. This module leverages outputs from OrthoFinder, selecting optimal gene families to create the ALE file for each gene family. Users can conveniently upload a time divergence tree, interactively specify WGD events for testing directly on the tree, and effortlessly generate Whale code. This streamlined process eliminates the need for users to delve into Julia scripting, ensuring a user-friendly experience.
• TimeTreeFetcher
  • This module simplifies the process of obtaining a species tree from TimeTree.org, especially when users are uncertain about the evolutionary relationships among studied species. By simply uploading a file containing species names, this module seamlessly communicates with TimeTree.org, providing users with two types of trees. The first type mirrors the sample tree structure found on TimeTree.org, while the second represents a tree constructed based on the median divergence time among studied species. This module offers a straightforward solution for users seeking clarity in their species relationships.

• Analysis

• KsDist
  • This module simplifies the identification of WGD events using Ks age distribution. Leveraging Data Preparation outputs, users customize selections in the configuration settings for tailored results. The module corrects paralog Ks distribution peaks with two methods: normal mixture model fitting and SiZer. It also utilizes relative rate tests to quantify substitution rate differences. Ideal for users exploring WGD events through Ks age distribution analysis.
• Collinearity
  • This module broadens the investigation of collinear relationships across all studied species, surpassing the capabilities of ksrates. It provides visualizations of collinear blocks. Additionally, users can delve into the exploration of putative ancestral regions (PARs) through clustering analysis, offering a more detailed and interactive exploration of the genomic architecture.
• TreeRecon
  • This module visualizes Whale output and posterior distributions of WGD retention rates (q) for potential WGDs under selected models.
• VizWGD
  • This module lets users customize the MCMCtree's time tree, or a ultrametic tree. Upload a tree file, click branches to add WGD events, and adjust colors and symbols. Highlight geological time regions with ease.

• Gallery

• Help

shinyWGD documentation built on April 4, 2025, 2:28 a.m.