To install mafft do the following.

1. download deb package from here

2. Create a folder to extra the package into.

mkdir extracted

3. Then unpack

dpkg-deb -x mafft_7.520-1_amd64.deb extracted/

4. cd into the extracted/usr folder and copy everything to /home/.hub_local/.

cd extracted/usr
cp -rf * /home/.hub_local/.

That should do it.