show-aligns: 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/show-aligns - from package: mummer

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

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