mafft-linsi: 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/lib/mafft/bin/mafft-linsi - from package: mafft

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