STRIKE: evaluation of protein MSAs using a single 3D structure

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

(2010) Michael L Sierk et al.   BMC BIOINFORMATICS

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

(2010) M. R. Aniba et al.   NUCLEIC ACIDS RESEARCH

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

(2008) Jean-François Taly et al.   BMC BIOINFORMATICS

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

(2008) Sitao Wu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE