Indel Reliability in Indel-Based Phylogenetic Inference

Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies

(2014) Eli Levy Karin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The top 100 papers

(2014) Richard Van Noorden et al.   NATURE

Transfer of noncoding DNA drives regulatory rewiring in bacteria

(2014) Yaara Oren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

(2012) Y. Lin et al.   BIOINFORMATICS

Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis

(2012) B. P. Blackburne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

(2012) Peng-tao Luan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments

(2012) Pravech Ajawatanawong et al.   NUCLEIC ACIDS RESEARCH

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

Re-Mind the Gap! Insertion – Deletion Data Reveal Neglected Phylogenetic Potential of the Nuclear Ribosomal Internal Transcribed Spacer (ITS) of Fungi

(2012) László G. Nagy et al.   PLoS One

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes

(2011) Yu Lin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

Modeling large regions in proteins: Applications to loops, termini, and folding

(2011) Aashish N. Adhikari et al.   PROTEIN SCIENCE

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

(2009) Rahul Satija et al.   BMC EVOLUTIONARY BIOLOGY

Alignment of Phylogenetically Unambiguous Indels in Shewanella

(2009) John P. McCrow   JOURNAL OF COMPUTATIONAL BIOLOGY

Large-Scale Parsimony Analysis of Metazoan Indels in Protein-Coding Genes

(2009) F. Belinky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stochastic models of sequence evolution including insertion—deletion events

(2009) István Miklós et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

(2008) Ádám Novák et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

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

(2008) A. Loytynoja et al.   SCIENCE