hmmalign: 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/hmmalign - from package: hmmer

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

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