Some new papers that may be of interest to people:
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.
Statistical Methods for Functional Metagenomic Analysis Based on Next-Generation Sequencing Data PhD thesis from Pookhao, Naruekamol
Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data
Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data