The LIBSHUFF Homepage

Welcome to the homepage of the LIBSHUFF analysis.  LIBSHUFF is a computer program designed to compare two libraries of 16S rRNA gene sequences and determine if they are significantly different.
DECEMBER 15th, 2003 : LIBSHUFF v1.1 CONTAINED AN ERROR. THE MOST COMMON RESULT OF THIS ERROR WAS INCREASED P-VALUES. THIS ERROR HAS BEEN FIXED IN THE CURRENT VERSION (1.2). PLEASE UPDATE YOUR SCRIPTS AND NOTIFY ANY APPLICABLE COLLEAGUES OF THE CHANGE. WE SINCERELY APOLOGIZE FOR ANY INCONVENIENCE THAT THIS ERROR MAY HAVE CAUSED.

For a web-based program for online LIBSHUFF analysis, use webLIBSHUFF

download LIBSHUFF:

LIBSHUFF perl program; right click to "save as" on your computer


preLIBSHUFF:

(DO NOT use with webLIBSHUFF)

PRELIBSHUFF perl program that formats a PHYLIP file into a sample file for use with LIBSHUFF

Directions for using PRELIBSHUFF (pdf; requires Adobe Acrobat)


LIBSHUFF documentation:

LIBSHUFF F.A.Q.: please read the frequently asked questions

LIBSHUFF tips: cautions for interpreting LIBSHUFF results

Bonferroni correction for experimentwise error (pdf; requires Adobe Acrobat)

A description of what the LIBSHUFF analysis is doing (pdf; requires Adobe Acrobat)

A simplified explanation of LIBSHUFF analysis (pdf; requires Adobe Acrobat)

Method 1: Creating a sample file - (pdf; uses GCG, Word, Excel, PHYLIP)

Method 2: Creating a sample file - (pdf; uses ClustalX, PHYLIP, Word)

Word Macro for formatting pileup output for DNADIST


LIBSHUFF links:

webLIBSHUFF,a web-based method of running LIBSHUFF

Perl Homepage, the programing language that is necessary to run LIBSHUFF

MacPerl Hompage for Macintosh OS9 perl users (OSX has perl installed by default)

Activestate Homepage for Windows perl users

PHYLIP Homepage, a suite of phylogeny programs by Dr. Felsenstein

Adobe Acrobat pdf reader

S-libshuff a C++ implementation of LIBSHUFF by Dr. Schloss

PLEASE NOTE:

THIS SOFTWARE IS PROVIDED BY THE AUTHORS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Updated October 17 2008