Copyright (C) 2006 SRI International

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
############################################################################

TIPS (Tree Inferred from Profile Scores)
http://www.pantherdb.org/downloads/
5/29/07

TIP an algorithm to build a protein family tree.  This tree-building algorithm is based on agglomerative clustering with a similarity measure derived from profile scoring.  TIPS can be used for large protein famililies, and due to its time scalability and accuracy, TIPS is being used in the large-scale PANTHER protein classification project.

More information can be found in the following publication:
Betty Lazareva-Ulitsky, Karen Diemer L., and Paul D. Thomas. 2005. On the quality of tree-based protein classification. Bioinformatics.  

http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1876?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=diemer&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT


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This has been compiled on the following systems:

Debian Linux  2.6.8-11-amd64-k8-smp, gcc 3.3.5

Solaris SunOS 5.8, gcc 3.0.3
   Because of the old version of gcc, the following had to be done on solaris:
   setenv LD_LIBRARY_PATH /usr/local/lib	

MacOS X Darwin 8.7.1, gcc version 4.0.1
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How to Compile code:

Precompiled code for Solaris and Linux exists in the Solaris/ and Linux/ directories.  This may or may not work for your system.

-To build on Solaris you have to invoke

>>make clean
>>make

This copies the binary to Solaris/

-To build on Linux you have to do

>>make clean
>>make PLATFORM=Linux

this copies the binary to Linux/

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Trouble shooting:

On solaris, we are using an old version of g++.  If your version
of g++ is more recent, you may run into compilation problems.

If so, then try replacing:
#ifdef __sun
with
#if 0.

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How to run TIPS:

To see the usage:
./TIPS

Command we use to generate trees for PANTHER:
TIPS -msa <pir_file> -prior <prior_file> -basename <output_name> -cut_using_distance 0.5 -pair_type 1 -score_matrix BLOSUM62 -use_are_as_branch_length 0

The prior file we use can be downloaded from: http://www.cse.ucsc.edu/research/compbio/dirichlets/uprior.9comp

the BLOSUM62 matrix can be downloaded from: ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62

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To test the your compliled TIPS code is owrking properly:

an example msa file has been included and is called: test.pir
exampel command: ./TIPS -msa test.pir -prior uprior.9comp -basename testout -cut_using_distance 0.5 -pair_type 1 -score_matrix BLOSUM62 -use_are_as_branch_length 0

This should execute correctly and produce the following files:
testout.tree_seqs
testout.nodes.tree
testout.profile
testout.SF0.profile
testout.SF1.profile
testout.SF2.profile
testout.SF3.profile
testout.SF4.profile
testout.SF5.profile
testout.SF6.profile
testout.SF7.profile

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Version History:
version 1.01 - now handles updated format for uprior.9comp file; also made minor change so that TIPS software has better compatability with Linux; includes test.pir so user can test code


If you have any questions, please contact us at: feedback@pantherdb.org