maf-sort: 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
/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/maf-sort - from package: last-align

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