clustalx: 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/clustalx - from package: clustalx

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

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