mafft-homologs: 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/mafft-homologs - from package: mafft

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