AliGROOVE – visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

Measuring guide-tree dependency of inferred gaps in progressive aligners

(2013) Salvador Capella-Gutiérrez et al.   BIOINFORMATICS

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

(2011) Maximilian P Nesnidal et al.   BMC GENOMICS

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont 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

Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life

(2011) Patrick Kück et al.   PLoS One

Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

(2010) Almir R Pepato et al.   BMC EVOLUTIONARY BIOLOGY

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

(2010) Patrick Kück et al.   Frontiers in Zoology

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Including secondary structure, fossils and molecular dating in the centipede tree of life

(2010) Jerome Murienne et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of acariform mites (Acari, Arachnida): Strong conflict between phylogenetic signal and long-branch attraction artifacts

(2010) Miroslawa Dabert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Spermatozoa of an Old World Ricinulei (Ricinoides karschii, Ricinoidae) with notes about the relationships of Ricinulei within the Arachnida

(2010) G. Talarico et al.   TISSUE & CELL

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The root of the East African cichlid radiations

(2009) Julia Schwarzer et al.   BMC EVOLUTIONARY BIOLOGY

INDELible: A Flexible Simulator of Biological Sequence Evolution

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

A Phylogenomic Approach to Resolve the Basal Pterygote Divergence

(2009) S. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

Noisy: Identification of problematic columns in multiple sequence alignments

(2008) Andreas WM Dress et al.   Algorithms for Molecular Biology

Recent developments in the MAFFT multiple sequence alignment program

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