protpars: 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/lib/phylip/bin/protpars - from package: phylip

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

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