clustalo: 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/clustalo - from package: clustalo

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

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