🧬 GRASP Ancestral Sequence Reconstruction (ASR) – Colab Pipeline

This repository provides a simple, user-friendly pipeline to perform Ancestral Sequence Reconstruction (ASR) using GRASP, as described in:
Foley, Gabriel, et al. “Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP).” PLOS Computational Biology 18.10 (2022): e1010633.

📓 What is this?
A ready-to-run Google Colab notebook that:

Aligns your input protein sequences

Builds a phylogenetic tree

Infers ancestral protein sequences at all internal nodes

Outputs all relevant files including alignment, tree, and reconstructed ancestors

No local installation required. Everything runs in the cloud!

🚀 Quick Start
Open the notebook: 📗 Grasp.ipynb

Upload your protein sequences in FASTA format (.fa or .fasta)

In the notebook, set the name of your input file
Then just run all cells.

📥 Input
A single FASTA file with protein sequences (amino acids)

Example:
>Sequence1
MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQ...
>Sequence2
MAQQQQQQQQLLSSSRTFLKIEGILNSNKDL...


📤 Output

The notebook automatically generates:

✅ Multiple sequence alignment (.fasta)

🌳 Phylogenetic tree of your sequences (.nwk)

🧠 A FASTA file containing ancestral sequences for all internal nodes

🧬 Annotated phylogenetic tree with ancestral node labels