MAFFT

MAFFT provides a console-based sequence alignment program for nucleotides and amino acids, offering various alignment methods for scientists to use.

As stated above, MAFFT only works in the Windows console, but it also comes with a ready-to-use Powershell script you can run. The advantage of this console application is that it can be called by any other Windows application.

Note that the application's speed is highly influenced by any running antivirus scans. In other words, if a virus analysis is currently running, expect delays when loading MAFFT's environment.

Despite that it only runs as a console application, working with MAFFT is not difficult at all. There are a few steps you need to take to process an input file and you are asked for answers to questions or input data at each step.

The first thing you need to do is enter the path of the input file. MAFFT is only compatible with specific FASTA files containing nucleotide and amino acid sequences.

Next, you must enter the name of the output FASTA file and choose between the available output formats. MAFFT puts various alternatives at your disposal, including Clustal, Fasta, and Phylip format, either in sorted or in the input order. Don't worry about the arguments, just select the desired option and MAFFT takes care of the rest.

There are various alignment strategies you can use, namely FFT-NS-1 and FFT-NS-2, G-INS-i, L-INS-i, or E-INS-i. If you are not sure about what the proper method is for your input file, just choose the "auto" option. Keep in mind that RNA structural alignment is not supported.