Here are a few tips on how to use the Delila programs.
There is a manual page for each Delila program. Think of each one as a power tool. It may have several input files and it has various controls. For example, the makelogo program has a control file makelogop, which stands for 'makelogo parameter file'. It affects how the the sequence logo will be generated.
To set up to do an analysis, I suggest that you make a directory and either make links or copies of the necessary files. You will need to know some Unix for this. After you have been able to run the programs by hand, I recommend that you make scripts to do things for you. By doing things this way, you can automate the analysis. If you need to change a parameter file, then you only need to rerun the script and you get the new figure. The programs are so fast that repeating things really is not too costly.
Unix links are made by the ln program (use 'man ln') but that is "backwards" from the way I think about it, so I wrote the 'lk' script.
It is best to put copies of the programs into a single binary directory and then set your 'path' to go through that directory.
You need to find your sequences in GenBank. One approach:
In the individual information package, when you run the demo files you are running a Unix script. The script is a text file that you can look at to see what programs were run. Each example sets up the necessary files and then runs the programs.
You can save enormous amounts of effort by using the atchange program.
origin: 1998 November 29
updated: 1999 August 24
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