t_coffee: 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/t_coffee - from package: t-coffee

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

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