🌳 Simple Phylogeny: Building Phylogenetic Trees

Simple Phylogeny is a bioinformatics tool that helps you construct basic phylogenetic trees from multiple sequence alignments. It's designed to infer evolutionary relationships between sequences, providing a visual representation of their divergence.

❓ What is Simple Phylogeny?

Simple Phylogeny takes a multiple sequence alignment (MSA) as input and uses distance-based methods (like Neighbor-Joining or UPGMA) to build a phylogenetic tree. It calculates the genetic distance between each pair of sequences and then groups them based on these distances, illustrating their evolutionary history.

  • Tree Construction: Builds phylogenetic trees from aligned sequences.
  • Evolutionary Relationships: Visualizes divergence and relatedness.
  • Distance-Based Methods: Uses common algorithms like Neighbor-Joining.

🎯 Why Use Simple Phylogeny? For Visualizing Evolutionary History

Simple Phylogeny is indispensable for:

  • 🔍 Inferring Ancestry: Understanding the evolutionary history and relationships among a set of genes or proteins.
  • 🧬 Species Classification: Aiding in the classification of organisms based on molecular data.
  • 📊 Identifying Clades: Grouping closely related sequences into clades.
  • 🎯 Comparative Genomics: Visualizing the divergence of homologous sequences across different species.
  • 📈 Educational Purposes: Providing a straightforward way to demonstrate phylogenetic principles.

🧑‍💻 How to Use Simple Phylogeny on Job Dispatcher: A Step-by-Step Guide

Follow these simple steps to construct a phylogenetic tree from your multiple sequence alignment:

1️⃣ Navigate to the Tool

  1. From the main menu, go to All Tools (or search for "Simple Phylogeny").
  2. Click the prominent Use Tool button located next to "Simple Phylogeny."

2️⃣ Input Your Multiple Sequence Alignment

  • Locate the input box (large text area) or the "upload a Sequence File" option.

  • Paste your multiple sequence alignment (MSA) in FASTA format or upload a FASTA file.

    >Human
MKTIIALSYIFCLVFADYKDDDDK
>Mouse
MKTVIALSYIFCLVFADYKDDDDK
>Rat
MKTVIALSYIFCLVFADYKDDDDK
>Chimpanzee
MKTIIALSYIFCLVFADYKDDDDK
>Dog
MKTVIALSYIFCLVFADYKDDDDK

  • Important: You can provide sequences either by typing into the text area OR by uploading a file, but not both simultaneously. Please clear one input to proceed.

3️⃣ Configure Parameters

  • 📝 Title: Provide a descriptive title for your job (e.g., "My Phylogenetic Tree").

  • 💡 Sequence Type: (Note: This tool typically expects aligned protein or nucleic acid sequences. The sequence type might be inferred from the alignment or selected if provided.)

  • 🌳 TREE FORMAT (tree): Choose the output format for the phylogenetic tree.

    • phylip - Default
    • nj (Clustal)
    • dist (Distance Matrix)
    • nexus (NEXUS)

  • 📏 DISTANCE CORRECTION (kimura): Apply Kimura's two-parameter correction for nucleotide sequences.

    • ON
    • OFF - Default

  • ✂️ EXCLUDE GAPS (tossgaps): Exclude positions containing gaps from distance calculations.

    • ON
    • OFF - Default

  • 📊 CLUSTERING METHODS (clustering): Select the clustering algorithm for tree construction.

    • Neighbour-joining - Default
    • UPGMA

  • 📈 PERCENT IDENTITY MATRIX (pim): Output a percent identity matrix.

    • ON
    • OFF - Default

4️⃣ Submit Your Job

  • Once your alignment is entered and parameters are set, click the Submit or Run button.

  • Your job will be dispatched to the EMBL-EBI Web Service. You will be automatically redirected to a Job Status page to monitor its progress.

5️⃣ Interpret Results

  • On the results page, you will find your generated phylogenetic tree (in the chosen format) and potentially a distance matrix.
  • The tree will visually represent the evolutionary distances and relationships among your sequences.
  • ⭐ Tip: Branch lengths on the tree typically represent evolutionary distance. Closely related sequences will have shorter branches connecting them.

💬 Need Help?

If you run into issues, please visit our Contact Us page for support. Happy tree building!