phmmer: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

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/phmmer - from package: hmmer

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