MAFFT for Windows - a multiple sequence alignment program

Install Ubuntu on Windows (steps 1–3) and subsequently install MAFFT on Ubuntu (steps 4–6).

Details: https://docs.microsoft.com/windows/wsl/install

On the Ubuntu window, run the following command to download MAFFT package.
```
$ wget https://mafft.cbrc.jp/alignment/software/mafft_7.526-1_amd64.deb 
```
To paste this command into the Ubuntu window, use right button of mouse. If it does not work, enable QuickEdit Mode.

Install the package by:

$ sudo dpkg -i mafft_7.526-1_amd64.deb 
[sudo] password for username: (Type the password that was set in step 2)

Check location and version number of MAFFT.

$ which mafft
/usr/bin/mafft

$ mafft --version
v7.526 (2024/Apr/22)

Suppose input file, eg, input.txt, is placed in C:\Users\yourname\DATA
This folder can be accessed from Ubuntu as /mnt/c/Users/yourname/DATA
In short, C: on Windows = /mnt/c on Ubuntu.
On Ubuntu window, change directory, cd, to the folder where input.txt is.
```
$ cd /mnt/c/Users/yourname/DATA
```
To check if input.txt actually exists in this folder, use the ls command.
```
$ ls
input.txt
```
Just type mafft to start a text-based interactive interface:
```
$ mafft
```
and follow the prompts to select input file, output file and options.
The output file has UNIX-style line-endings. If Windows style is preferable, then open the file with WordPad to convert it.

On Ubuntu terminal, type:
```
$ mafft (options) input.txt > output.txt
```
All features can be used in this mode.

If you use user-define guide tree, the merge option, etc, then install the Ruby package by:
```
$ sudo apt install ruby 
```
Ruby can also be used to convert line endings to Windows style. On Ubuntu terminal,
```
$ ruby -pe 'sub("\n","\r\n")' output.txt > output.windows.txt 
```

Multiple alignment program for amino acid or nucleotide sequences