raxmlHPC-PTHREADS-SSE3: 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-SSE3 - from package: raxml

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

Error in other languages:
raxmlHPC-PTHREADS-SSE3: bevel nie gevind nie
raxmlHPC-PTHREADS-SSE3: comandă negăsită
raxmlHPC-PTHREADS-SSE3: comando não encontrado
raxmlHPC-PTHREADS-SSE3: commande introuvable
raxmlHPC-PTHREADS-SSE3: command not found
raxmlHPC-PTHREADS-SSE3: käsku ei ole
raxmlHPC-PTHREADS-SSE3: không tìm thấy lệnh
raxmlHPC-PTHREADS-SSE3: komanda nerasta
raxmlHPC-PTHREADS-SSE3: Kommando nicht gefunden.
raxmlHPC-PTHREADS-SSE3: kommandot finns inte
raxmlHPC-PTHREADS-SSE3: komut yok
raxmlHPC-PTHREADS-SSE3: nie znaleziono polecenia
raxmlHPC-PTHREADS-SSE3: níor aimsíodh an t-ordú
raxmlHPC-PTHREADS-SSE3: no se encontró la orden
raxmlHPC-PTHREADS-SSE3: no s'ha trobat l'ordre
raxmlHPC-PTHREADS-SSE3: opdracht niet gevonden
raxmlHPC-PTHREADS-SSE3: parancs nem található
raxmlHPC-PTHREADS-SSE3: perintah tidak ditemukan
raxmlHPC-PTHREADS-SSE3: príkaz nenájdený
raxmlHPC-PTHREADS-SSE3: příkaz nenalezen
raxmlHPC-PTHREADS-SSE3: команда не найдена
raxmlHPC-PTHREADS-SSE3: командата не е открита
raxmlHPC-PTHREADS-SSE3: 命令找不到
raxmlHPC-PTHREADS-SSE3: コマンドが見つかりません