jalview: 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/jalview - from package: jalview

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

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