Updated readme

README.md

@@ -2,6 +2,18 @@
 
 Niels W. Hanson, Kishori M. Konwar, Shang-Ju Wu, and Steven J. Hallam
 
+## Updates
+
+**November 27, 2014**: MetaPathways v2.5 released with upgrades to the pipeline:
+
+* LAST homology searches with BLAST-equivalent output and E-values
+* Reads per kilobase per million mapped (RPKM) coverage measure for Contig annotations calculated from raw reads (`.fastq`) or mapping files (`.SAM`) using [bwa](http://bio-bwa.sourceforge.net)
+* Addition of the [CAZy sequence database](http://www.cazy.org) as a new compatible functional hierachy
+* GUI Keyword-search from annotation subsetting and projection onto different functional hierarcies (KEGG, COG, SEED, MetaCyc, and now CAZy)
+
+[See the wiki](https://github.com/hallamlab/metapathways2/wiki) for more information.
+
+
 ## Abstract
 
 The development of high-throughput sequencing technologies over the past decade has generated a tidal wave of environmental sequence information from a variety of natural and human engineered ecosystems. The resulting flood of infor- mation into public databases and archived sequencing projects has exponentially expanded computational resource requirements rendering most local homology-based search methods inefficient. We recently introduced MetaPathways v1.0, a modular annota- tion and analysis pipeline for constructing environmental Path- way/Genome Databases (ePGDBs) from environmental sequence information capable of using the Sun Grid engine for external resource partitioning. However, a command-line interface and facile task management introduced user activation barriers with concomitant decrease in fault tolerance.
@@ -10,10 +22,10 @@ Here we present MetaPathways v2.0 incorporating a graphical user interface (GUI)
 
 ## Installation
 
-MetaPathways v2.0 requires Python 2.6 or greater and [Pathway Tools](http://bioinformatics.ai.sri.com/ptools/) developed by SRI International for full functionality.
+MetaPathways v2.5 requires Python 2.7 or greater and [Pathway Tools](http://bioinformatics.ai.sri.com/ptools/) developed by SRI International for full functionality.
 
-The MetaPathways Python codebase as well as the GUI code is self-contained in this GitHub distro.
+The MetaPathways Python codebase as well as the compiled GUI binaries for Mac OSX and Ubuntu are self-contained in this GitHub distro. GUI source code can be [obtained here](https://github.com/hallamlab/MetaPathwaysGUI).
 
-Please see the [MetaPathways v2.0 wiki](https://github.com/hallamlab/metapathways2/wiki) for more installation and usage information.
+Please see the [MetaPathways v2.5 wiki](https://github.com/hallamlab/metapathways2/wiki) for more installation details.
 
 A template [MetaPathways_DBs.zip (**Updated: October 2014**)](https://www.dropbox.com/s/ye3kpve041e0r39/MetaPathways_DBs.zip?dl=0) contains starter protein and taxonomic databases