Running PhyloSift

Before you can run PhyloSift, you must download it. Click “Download PhyloSift Here” in the quick links sidebar on the right hand side of this webpage for a direct file download. Or, you can find more detailed and advanced downloading instructions here:

Downloading PhyloSift


Most users will want to run their own environmental metagenome data through PhyloSift. Guides and step-by-step tutorials can be found here:

Executing PhyloSift – input data and command line instructions

Processing Multiplexed Samples in PhyloSift

Statistically assessing for presence/absence of a taxon using Bayes factor tests

Metagenome Analysis Tutorial using PE-Illumina Data


A description of the PhyloSift output files and directories can be found here:

PhyloSift Outputs


Power users may want to incorporate their own marker genes, mine genomes, or generate simulation datasets. Workflows for these PhyloSift features can be found here:

Building PhyloSift marker packages (The Monkey)

Generating simulated datasets (The Kangaroo)

Expanding PhyloSift marker databases with new genome data (UpdateDB)


Advanced users may also want to alter the default program settings used in the PhyloSift pipeline. This can be accomplished by inputing a phylosiftrc file on any command line run.

PhyloSift Run Control File – Instructions