trees2NEXUS: 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/fastdnaml/bin/trees2NEXUS - from package: fastdnaml

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

Error in other languages:
trees2NEXUS: bevel nie gevind nie
trees2NEXUS: comandă negăsită
trees2NEXUS: comando não encontrado
trees2NEXUS: commande introuvable
trees2NEXUS: command not found
trees2NEXUS: käsku ei ole
trees2NEXUS: không tìm thấy lệnh
trees2NEXUS: komanda nerasta
trees2NEXUS: Kommando nicht gefunden.
trees2NEXUS: kommandot finns inte
trees2NEXUS: komut yok
trees2NEXUS: nie znaleziono polecenia
trees2NEXUS: níor aimsíodh an t-ordú
trees2NEXUS: no se encontró la orden
trees2NEXUS: no s'ha trobat l'ordre
trees2NEXUS: opdracht niet gevonden
trees2NEXUS: parancs nem található
trees2NEXUS: perintah tidak ditemukan
trees2NEXUS: príkaz nenájdený
trees2NEXUS: příkaz nenalezen
trees2NEXUS: команда не найдена
trees2NEXUS: командата не е открита
trees2NEXUS: 命令找不到
trees2NEXUS: コマンドが見つかりません