Principle Programs

The main programs are genewise, genewisedb, estwise, estwisedb. These all have basically the same running mode

%genewise protein-file dna-file

A number of options are common to these programs from the point of view of how they run

-help

verbose help of all options

-version

show version and compile info

-silent

No messages on stderr, whether reports or warnings

-quiet

No reports or information messages on stderr

-erroroffstd

No warning messages to stderr, but reports are still issued

-errorlog

[file] Log warning messages to file (useful for sending to me)

You will probably want to read the 2.1 common modes of usage section as well