version 2.0

CHANGELOG

+DOGMA 2.0
+=========
+
+- added reference sets for bacteria, archae
+- expanded support for different Pfam versions
+- usage of order for UProC (proteome only)
+- removing clan collapse

README.md

+DOGMA
+====
+
+DOGMA is a program for fast and easy quality assessment of 
+transcriptome and proteome data based on conserved protein domains.
+
+Requirements
+------------
+
+We try to keep the dependencies as little as possible. 
+Current dependencies are (but you will just need one of them):
+
+- UProC (http://uproc.gobics.de/)
+OR
+- pfam_scan.pl (ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/)
+
+
+Furthermore you will need a core set to run DOGMA. 
+We provide several precomputed core sets for different clades here:
+
+http://domainworld.uni-muenster.de/DOGMA.html
+
+Unfortunately the developers of UProC do not provide databases for the newer pfam versions. 
+We therefore constructed them ourselves and tested them in combination with DOGMA (no warranty for any other use).
+They can be downloaded from our website (see link above).
+
+
+Usage
+-----
+
+Please take a look at the User Manual for a detailed description.
+
+
+Citation
+--------
+
+If you used DOGMA in your project please cite our publication:
+
+Elias Dohmen, Lukas P.M. Kremer, Erich Bornberg-Bauer, and Carsten Kemena, DOGMA: domain-based transcriptome and proteome quality assessment, 
+Bioinformatics (2016) 32 (17): 2577-2581, first published online May 5, 2016, doi:10.1093/bioinformatics/btw231 
+
+http://bioinformatics.oxfordjournals.org/content/32/17/2577
+
+
+Problems, Bugs & Suggestions
+----------------------------
+
+We try our best not to have any bugs in the code, unfortunately some will
+probably avoid us and will not be detected. 
+
+If you encounter one, please be so kind and let us know. 
+
+Also if you have any questions feel free to contact us by email:
+
+Elias Dohmen (e.dohmen[ at ]uni-muenster.de) or 
+
+Carsten Kemena (c.kemena[ at ]uni-muenster.de)
+
+