[DOC] update de_novo, auto_rec, and auto_dom tools.
[DOC] update de_novo, auto_rec, and auto_dom tools.

bgruening/gemini,bpow/gemini,udp3f/gemini,heuermh/gemini,bpow/gemini,bw2/gemini,heuermh/gemini,bgruening/gemini,heuermh/gemini,heuermh/gemini,xuzetan/gemini,udp3f/gemini,brentp/gemini,arq5x/gemini,bgruening/gemini,bgruening/gemini,arq5x/gemini,bpow/gemini,brentp/gemini,bw2/gemini,xuzetan/gemini,bw2/gemini,udp3f/gemini,arq5x/gemini,brentp/gemini,bpow/gemini,xuzetan/gemini,bw2/gemini,xuzetan/gemini,brentp/gemini,udp3f/gemini,arq5x/gemini