TABLE 1.

Features from preexisting software that have been integrated into mothura

Existing toolDescriptionImplementation in mothurReference(s)
Pyrosequencing pipeline (RDP)Online tool that trims and deconvolutes sequences using user-supplied dataStand-alone implementation; increased speed; greater flexibility; additional screening options3
NAST, SINA, and RDP alignersOnline tools that align user-supplied sequences with specific databasesStand-alone implementation; can utilize multiple processors; increased speed; greater flexibility; open source3-5, 20
DNADISTCalculates pairwise distances between sequences (does not penalize for gaps)Can utilize multiple processors; more efficient use of RAM; various ways to penalize gaps6
DOTUR and CD-HITAssigns sequences to OTUs, constructs sampling curves, and estimates richness and diversityMore efficient clustering; requires less memory; additional calculators; greater flexibility10, 22
SONSCalculates estimates of the fraction and richness of OTUs shared between communitiesGenerates dendrograms, heat maps, and Venn diagrams; additional calculators; greater flexibility23
∫-LIBSHUFFUses the Cramer-von Mises statistic to test whether two communities have the same structureEliminates the need for a sorted distance matrix; can specify pairwise comparisons25, 26
TreeClimberUses a parsimony-based test to determine whether two or more communities have the same structureGreater flexibility; can specify pairwise comparisons14, 15,24
UniFracCompares the phylogenetic distance between communities to detect differences in community structureStand-alone implementation; greater flexibility; can input bootstrap trees12
  • a In all cases, modifications have been made to the mothur implementation of the algorithms for greater flexibility, speed, and resource utilization.