MAFFT

MAFFT is a cool tool that helps scientists with sequence alignment for both nucleotides and amino acids. It’s all console-based, which means you’ll be typing commands in the Windows console to get things done.

Getting Started with MAFFT

So here’s the deal: MAFFT runs only in the Windows console, but don’t worry! It comes with a handy Powershell script that you can use right away. The neat thing about this console app is that it can be accessed by any other Windows application, making it pretty flexible.

Performance Notes

Just a heads-up: the speed of MAFFT can slow down if your antivirus scans are running at the same time. So, if you notice some lag when loading MAFFT, check if your virus scanner is busy.

Using MAFFT Made Easy

You might think using a console app sounds tough, but it’s actually pretty straightforward! You just need to follow a few steps to process your input file. Each step will ask you questions or for data input—easy peasy!

Input File Requirements

The first thing you’ll do is enter the path of your input file. Just remember, MAFFT works with specific FASTA files that contain nucleotide and amino acid sequences.

Choosing Your Output

Next up, you’ll need to name your output FASTA file and choose from different output formats. MAFFT gives you plenty of options like Clustal, Fasta, and Phylip format—both sorted and unsorted. Don’t stress over the details; just pick what you want, and MAFFT takes care of the rest!

Selecting Alignment Strategies

You’ve got several alignment strategies available too! Options include FFT-NS-1 and FFT-NS-2, G-INS-i, L-INS-i, or E-INS-i. If you're unsure which one to pick for your input file, just go with the “auto” option—it’s there to help! Just keep in mind that RNA structural alignment isn’t supported.