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[modeller_usage] help at first script

I am a new user of modeller9v3 and I can't write the first script with which I
will search for sequences similar to the target one. I also consult the manual
of modeller6v2, will I confuse? If I have understood well, the appropriate
command is sequence_search which has many options. I must use all the options?
I can't understand the syntax of the command, i.e I must type mod9v3 before the
command, but I read that the syntax is mod9v3 script_ .top. This script what
does it contain?    (I can't understand anything becose I start now to deal
with bioinformatics). Please help me.
Thank you very much,