bl2seq: 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/bl2seq - from package: blast2
/usr/share/ncbi-blast+/bin/bl2seq - from package: ncbi-blast+-legacy

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

Error in other languages:
bl2seq: bevel nie gevind nie
bl2seq: comandă negăsită
bl2seq: comando não encontrado
bl2seq: commande introuvable
bl2seq: command not found
bl2seq: käsku ei ole
bl2seq: không tìm thấy lệnh
bl2seq: komanda nerasta
bl2seq: Kommando nicht gefunden.
bl2seq: kommandot finns inte
bl2seq: komut yok
bl2seq: nie znaleziono polecenia
bl2seq: níor aimsíodh an t-ordú
bl2seq: no se encontró la orden
bl2seq: no s'ha trobat l'ordre
bl2seq: opdracht niet gevonden
bl2seq: parancs nem található
bl2seq: perintah tidak ditemukan
bl2seq: príkaz nenájdený
bl2seq: příkaz nenalezen
bl2seq: команда не найдена
bl2seq: командата не е открита
bl2seq: 命令找不到
bl2seq: コマンドが見つかりません