shuffleseq: 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/shuffleseq - from package: emboss

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

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