raxmlHPC-PTHREADS: 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/raxmlHPC-PTHREADS - from package: raxml

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

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