ali2gff: 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/ali2gff - from package: gff2aplot

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

Error in other languages:
ali2gff: bevel nie gevind nie
ali2gff: comandă negăsită
ali2gff: comando não encontrado
ali2gff: commande introuvable
ali2gff: command not found
ali2gff: käsku ei ole
ali2gff: không tìm thấy lệnh
ali2gff: komanda nerasta
ali2gff: Kommando nicht gefunden.
ali2gff: kommandot finns inte
ali2gff: komut yok
ali2gff: nie znaleziono polecenia
ali2gff: níor aimsíodh an t-ordú
ali2gff: no se encontró la orden
ali2gff: no s'ha trobat l'ordre
ali2gff: opdracht niet gevonden
ali2gff: parancs nem található
ali2gff: perintah tidak ditemukan
ali2gff: príkaz nenájdený
ali2gff: příkaz nenalezen
ali2gff: команда не найдена
ali2gff: командата не е открита
ali2gff: 命令找不到
ali2gff: コマンドが見つかりません