mafft: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/mafft - from package: mafft
/usr/lib/mafft/bin/mafft - from package: mafft

You may install the required package with command apt-get install {package}

Error in other languages:
mafft: bevel nie gevind nie
mafft: comandă negăsită
mafft: comando não encontrado
mafft: commande introuvable
mafft: command not found
mafft: käsku ei ole
mafft: không tìm thấy lệnh
mafft: komanda nerasta
mafft: Kommando nicht gefunden.
mafft: kommandot finns inte
mafft: komut yok
mafft: nie znaleziono polecenia
mafft: níor aimsíodh an t-ordú
mafft: no se encontró la orden
mafft: no s'ha trobat l'ordre
mafft: opdracht niet gevonden
mafft: parancs nem található
mafft: perintah tidak ditemukan
mafft: príkaz nenájdený
mafft: příkaz nenalezen
mafft: команда не найдена
mafft: командата не е открита
mafft: 命令找不到
mafft: コマンドが見つかりません