LIBSHUFF Frequently Asked Questions (FAQ)
Last updated: November 8, 2002

Q: Can I run LIBSHUFF on my machine without installing Perl?
A: No.  The LIBSHUFF program found on this website is only a script and must be run within the Perl environment.

Q: Why Perl?  Aren't there any number of better programming languages out there?
A: Probably.  Unfortunately, we're not skilled programmers and we wanted to write a script that would run on nearly every operating system.  Perl was relatively straightforward to learn and seems to apply to a wide range of operating systems.

Q: The method for producing a "sample" file on the website seems overly long and complex.  Aren't there easier ways to do it?
A: The particular method first described on the website was derived from the way we originally prepared the sample files.  Since then, we have become aware of alternative methods.  Users are encouraged to contact us with their own particular method if it does not appear on the website, provided the sample file is compatible with the current script.  It is possible that we will add your particular protocol to the website.

Q: How many sequences do I need in my libraries to run LIBSHUFF?
A: The more the better.  Unfortunately, that's not the answer you want.  Around 50 sequences in each library appears sufficient to distinguish libraries when they are obviously different.  If the libraries appear more closely related, you will want to add more sequences.

Q: How do you create the graphs using the data in the "coverages" and "results" output files?
A: We have used a number of graphing programs, including CricketGraph, DeltaGraph, and Microsoft Excel.  To create graphs similar to those in our publications, place "d" on the X-axis, "X" and "XY" on the Y-axis, and "diff-X/XY" and "95% XY" on the secondary Y-axis.  To plot the reciprocol comparison, simply substitute the data in "Y", "YX", "diff-Y/YX", and "95% YX" on the proper axes

Q: I'm using a PC to run LIBSHUFF under the ActiveState Perl environment.  Every time I run the analysis, the window closes before I have time to read the p-values!  How can I stop this?
A: Open a separate window before running the program by selecting "Run" from the Start Menu and typing "command".  Once this window is open, you can change directories using the "cd" command.  Once you are in the folder containing the LIBSHUFF script and your sample file, you can run the script by typing, "perl libshuff.pl".

Q: I noticed that you just updated the LIBSHUFF script.  Is there a listserv or other way that I can be notified of changes to this analysis?
A: Send an email to "drsingle_at_email.unc.edu" with LIBSHUFF in the title to be placed on a list.  If we do another update, we will send you an email telling you (replace the "_at_" with an "@" to get the correct email address; I'm trying to avoid getting on mailing lists.)

Q: Where can I learn more about LIBSHUFF?
A: Look for the next edition of the Manual of Microbial Ecology Manual.  A chapter on the LIBSHUFF method will appear there.

Q: How do I cite LIBSHUFF in a publication?
A: Users of the program may cite the original publication:
        Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. B. Whitman. 2001. Quantitative comparisons
        of 16S rDNA sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4373-4376.

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