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

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

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