MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulates a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built.
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BMC Genomics. 2013 Jun 22;14:419. doi: 10.1186/1471-2164-14-419.
Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
Riesenfeld SJ, Pollard KS.