alf: 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/alf - from package: seqan-apps
/usr/lib/seqan/bin/alf - from package: seqan-apps

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

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