mummer-annotate: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

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/mummer-annotate - from package: mummer

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