cdhit-est: 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/cdhit-est - from package: cd-hit

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

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