phyml: 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/phyml - from package: phyml

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

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