Phylogenetic Profiling and Visualization of Gene Presence/Absence

This Colab-based tool automates the process of identifying the phylogenetic distribution of one or more genes across a user-defined set of genomes. It generates a presence/absence matrix and visualizes it alongside a taxonomic tree as a heatmap.

🚀 What it does

• 🧬 Accepts a set of protein sequences
• 🌍 Accepts a list of target organisms (or a short default list is available)
• ⬇️ Automatically retrieves proteomes (.faa files) from NCBI RefSeq
• 🧪 Runs BLASTP searches to detect gene presence
• 📊 Builds a presence/absence matrix
• 🌳 Constructs a taxonomic tree from NCBI
• 🎨 Plots a heatmap aligned to the tree

All of this is performed entirely in Google Colab — no local installation required.

---

📥 Input Files

You need to upload two files to the Colab environment before running the notebook:

1. query_genes.txt — Gene input file (FASTA or UniProt IDs)

This file can be provided in either of the following formats:

Option A – Protein FASTA file

A standard FASTA file containing one or more amino acid sequences. Each entry should have:

• A header line beginning with >gene_name
• The sequence on one or more lines

Option B – List of UniProt IDs

A plain text file with one UniProt ID per line. The notebook will automatically download the corresponding protein sequences.

2. organism_list.txt — Target species list

A plain text file with one organism name per line. These should be recognized species from NCBI.

📦 Don't have a list?
If no file is uploaded, the notebook will fall back to a default list of representative organisms, which includes a few common model species across different branches of life.

📓 How to use it

👉 Open the notebook in Colab

Steps:

1. Upload query_genes.txt and organism_list.txt
2. Run the notebook cells
3. Collect outputs:
   • CSV matrix: profile.csv
   • Heatmap figure: tree_and_heatmap.png