Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics

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

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

(2010) Olga K. Kamneva et al.   Genome Biology and Evolution

Impact of Indels on the Flanking Regions in Structural Domains

(2010) Zheng Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance

(2009) Zhengyuan Wang et al.   BMC EVOLUTIONARY BIOLOGY

A Guide to Template Based Structure Prediction

(2009) Xiaotao Qu et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

(2009) K. Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in Bacteria

(2009) L. Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0

(2009) Cory L. Strope et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

(2009) Robert K. Bradley et al.   PLoS One

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of antsBlochmannia floridanus

(2008) L. GÓMEZ-VALERO et al.   MOLECULAR ECOLOGY

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