hmm2align: 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/hmm2align - from package: hmmer2

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

Error in other languages:
hmm2align: bevel nie gevind nie
hmm2align: comandă negăsită
hmm2align: comando não encontrado
hmm2align: commande introuvable
hmm2align: command not found
hmm2align: käsku ei ole
hmm2align: không tìm thấy lệnh
hmm2align: komanda nerasta
hmm2align: Kommando nicht gefunden.
hmm2align: kommandot finns inte
hmm2align: komut yok
hmm2align: nie znaleziono polecenia
hmm2align: níor aimsíodh an t-ordú
hmm2align: no se encontró la orden
hmm2align: no s'ha trobat l'ordre
hmm2align: opdracht niet gevonden
hmm2align: parancs nem található
hmm2align: perintah tidak ditemukan
hmm2align: príkaz nenájdený
hmm2align: příkaz nenalezen
hmm2align: команда не найдена
hmm2align: командата не е открита
hmm2align: 命令找不到
hmm2align: コマンドが見つかりません