nwnsi: 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/nwnsi - from package: mafft

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

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