Fig. 4

Comparison of UPP variants on fragmentary datasets. We show average a alignment error and b ΔFN tree error for UPP (Default), UPP (Default, NoDecomp), UPP-random (Default), and UPP-random (Default, NoDecomp) for the fragmentary datasets. The backbone is not restricted to full-length sequences in UPP-random, and so it allows fragmentary sequences in the backbone set. UPP-random (Default, NoDecomp) failed to align at least one dataset from each of the RNASim 10K, Indelible 10K, and CRW model conditions. UPP (Default, NoDecomp) failed to align at least one dataset from each of the ROSE NT, RNASim 10K, and Indelible 10K model conditions. ML trees were estimated using FastTree under the general time reversible model