GUPPY results: Edge differences, edgePCA, phylogenetic diversity

Results from guppy software:, based on the output of Phylosift (Darling et al., PeerJ 2014), a method that extracts reads matching marker genes from WGS metagenomes and use them for phylogenetic placement on the Tree of Life to estimate the abundance of taxa present in a microbiome, GUPPY produces a matrix of edge differences of placement probability mass, i.e. "the differences between proportions of phylogenetic placements on either side of each internal edge of the reference phylogenetic tree" (Matsen & Evans, PLOS One 2013). This can be used to compute phylogenetic diversity within samples (aplha diversity) and represent diversity between samples (beta diversity) using edge principal component analysis (edgePCA).Comparison of results involving 24 original samples from the Philippines and meta-analyses with extended datasets including 7 or 9 individuals from the USA are also provided in the *.datasets.* foldersScripts used to analyse these results can be found on GitHub: https://github.com/flass/microbiomes/tree/master/scripts/phylosiftThis work was published in the journal Molecular Ecology doi: 10.1111/mec.1443