muscle: 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/muscle - from package: muscle

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

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