update

README

@@ -12,29 +12,16 @@ It uses the following criteria:
 
 The software is primarily maintained by Brian Haas at the Broad Institute and Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO). It is integrated into other related software such as Trinity, PASA, EVidenceModeler, and Trinotate.
 
-Full documentation is provided at: http://transdecoder.sf.net
+Full documentation is provided at: http://transdecoder.github.io
 
 ===========================
 To build just TransDecoder:
 
-Please make sure you read http://transdecoder.sf.net before proceeding.
+Please make sure you read http://transdecoder.github.io before proceeding.
 
    %  make
 
-To leverage the included PFAM data:
-
-   Be sure to have hmmer installed: http://hmmer.janelia.org/
-
-   % make prep_pfam
-
-To leverage MPI using ffindex:
-
-   % make all
-
 
 See sample_data/ directory for example usage.
 
 
-Notes:
-
-Binary PFAM database was prepared using PfamA and PfamB and then compressed using HMMER Version Easel h3.0 (March 2010)

Release.Notes

@@ -1,3 +1,18 @@
+
+## 2015-01-26   v2.0 release
+
+-overhauled the build
+    -removed the active searching of Pfam and all MPI-related funcitonality
+    -runs in 2 phase:
+        -TransDecoder.LongOrfs : extracs the long ORFs
+        -TransDecoder.Predict : predicts the likely coding regions among the ORFs
+            -step can use Pfam and blastp search results (blast support is a new addition)
+    -run Pfam and/or BlastP searches directly or try using "HPC GridRunner" (http://HpcGridRunner.github.io)
+
+-moved to github 
+
+
+
 ## 2014-07-04
 
 -added 'make simple' to build just the essential components involving parafly and cdhit