PMC

(a) Regions of the 16S ribosomal RNA included in this analysis. Start and end positions refer to positions in the Greengenes alignment and v regions indicate the variable regions included in each simulated amplicon. Sliced amplicons that would overlap entirely with other sliced amplicons are not included. Only full-length reads were used in analysis of the V9 region as the full-length amplicon is shorter than 150 bases. (b) Principal coordinates analysis of Pearson correlation coefficients between tip-to-tip distances in pairs of phylogenetic trees constructed from differentially sliced alignments. Points are colored by amplicon length. Points representing trees generated from full-length sequences are circled in white to indicate their position when obscured by other points. (c) Principal coordinates analysis of Pearson correlation coefficients between tip-to-tip distances in pairs of phylogenetic trees constructed from differentially sliced alignments. Points are colored by the first variable region encountered in the differentially sliced alignments. Points representing trees generated from full-length sequences are circled in white to indicate their position when obscured by other points.