Resources

Human microbiome journal club Mendeley library – papers presented in journal club and much, much more

AXIOME – Automation, Extension, and Integration Of Microbial Ecology: Helper tools to make managing numerical ecology pipelines easier

MetaHIT – Human Microbiome Live News – if you want to stay on top of microbiome research and news

SmashCommunity by M. Arumugam – a tool for quantitative metagenomic annotation

Berkley Phylogenomic Group page

MG-RAST – the metagenomics analysis server

OMI – open microbiome initiative

The BioWeatherMap Initiative – mapping geographical and temporal patterns of microbial life

mothur – microbial ecology analysis

QIIME – quantitative insights into microbial ecology

pplacer – phylogenetic placement of sequencing reads on a reference tree, applying likelyhood-based approaches to large sequence sets

iTOL – interactive tree of life is an online tool for the display and manipulation of phylogenetic trees

iSEEM – integrating statistical evolutionary and ecological approaches to metagenomics

HMP dacc – human microbiome project data collection management and tools. Look here for manuals, protocols and tools

PhylOTU – identifying microbial OTUs from metagenomic data

IMG – integrated microbial genomes resource