seqan_tcoffee: 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/seqan_tcoffee - from package: seqan-apps
/usr/lib/seqan/bin/seqan_tcoffee - from package: seqan-apps

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