hmmlogo: 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/hmmlogo - from package: hmmer

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

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