The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

(2008) Kazutaka Katoh et al.   BMC BIOINFORMATICS

The role of positive selection in determining the molecular cause of species differences in disease

(2008) Jessica J Vamathevan et al.   BMC EVOLUTIONARY BIOLOGY

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

(2008) R. A. Studer et al.   GENOME RESEARCH

How Well Does the HoT Score Reflect Sequence Alignment Accuracy?

(2008) Barry G. Hall   MOLECULAR BIOLOGY AND EVOLUTION

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE