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

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

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