Unearthing the evolutionary relationships between organisms can be a daunting task. But with some powerful tools, this can be done effeciently. In this tutorial, we will learn how to align protein sequences, construct a phylogenetic tree, and create stunning visualizations with minimal effort.

## Gathering the Toolbox

First things first, we need to install the right tools:

- Python with BioPython: We assume you have Python. Add BioPython using pip (`pip install biopython`).
- [MAFFT](https://mafft.cbrc.jp/alignment/software/): A speedster for multiple sequence alignment.
- [FastTree](http://www.microbesonline.org/fasttree/): Your ally to build approximate maximum-likelihood phylogenetic trees.
- [iTOL](https://itol.embl.de/): A web-based tool for crafting captivating phylogenetic tree visualizations. No installation required!

Ensure MAFFT and FastTree are accessible in your system's PATH. **Conda is highly recommended.**

## Fast Alignment with MAFFT

Here's a compact Python script for alignment with MAFFT:

from Bio.Align.Applications import MafftCommandline

# Input and output files
input_file = 'sequences.fasta'
alignment_file = 'aligned_sequences.fasta'

# Align sequences using MAFFT with 4 threads
mafft_cline = MafftCommandline(input=input_file)
mafft_cline.thread = 4
stdout, stderr = mafft_cline()

with open(alignment_file, "w") as handle:
    handle.write(stdout)

## Building Trees with FastTree

FastTree, known for its speed, can handle large datasets and quickly builds approximate maximum-likelihood trees. However, for smaller datasets, full maximum-likelihood programs might offer more accuracy.

Here's how to use FastTree in Python:

import subprocess

# Output file for the tree
tree_file = 'phylogenetic_tree.newick'

# Build the tree using FastTree
cmd = ["FastTree", alignment_file]
with open(tree_file, "w") as outfile:
    subprocess.call(cmd, stdout=outfile)

Or in your terminal

FastTree aligned_sequences.fasta > phylogenetic_tree.newick

## Bringing Trees to Life with iTOL

Once we've constructed our tree, it's time to visualize it with iTOL. Just upload your Newick file and start crafting your phylogenetic masterpiece!

## The Wrap-up

We've seen how to perform fast and efficient phylogenetic analysis with Python, MAFFT, FastTree, and iTOL. Each tool has its strengths and limitations, but together they create a formidable toolbox for bioinformatics.