A perennial problem in the analysis of environmental sequence information is the assignment of reads or assembled sequences, e.g. contigs or scaffolds, to discrete taxonomic bins. In the absence of reference genomes for most environmental microorganisms, the use of intrinsic nucleotide patterns and phylogenetic anchors can improve assembly-dependent binning needed for more accurate taxonomic and functional annotation in communities of microorganisms, and assist in identifying mobile genetic elements or lateral gene transfer events.