clustalw: 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/clustalw - from package: clustalw

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

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