FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

(2014) Eduardo Larriba et al.   FUNGAL GENETICS AND BIOLOGY

Phylogenetic relationships of yellowjackets inferred from nine loci (Hymenoptera: Vespidae, Vespinae, Vespula and Dolichovespula)

(2014) Federico Lopez-Osorio et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dynamic evolution of mitochondrial ribosomal proteins in Holozoa

(2014) Bettina M. Scheel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

2matrix: A Utility for Indel Coding and Phylogenetic Matrix Concatenation

(2014) Nelson R. Salinas et al.   Applications in Plant Sciences

Mitochondrial genomes to the rescue – Diurodrilidae in the myzostomid trap

(2013) Anja Golombek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of the Elopomorpha (Teleostei): Evidence from six nuclear and mitochondrial markers

(2013) Jhen-Nien Chen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular Phylogeny of Echiuran Worms (Phylum: Annelida) Reveals Evolutionary Pattern of Feeding Mode and Sexual Dimorphism

(2013) Ryutaro Goto et al.   PLoS One

Automatic categorization of diverse experimental information in the bioscience literature

(2012) Ruihua Fang et al.   BMC BIOINFORMATICS

Comparing the mitochondrial genomes of Wolbachia-dependent and independent filarial nematode species

(2012) Samantha N McNulty et al.   BMC GENOMICS

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Phylogenetic analysis of ticks (Acari: Ixodida) using mitochondrial genomes and nuclear rRNA genes indicates that the genus Amblyomma is polyphyletic

(2012) Thomas D. Burger et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole-genome sequence of Schistosoma haematobium

(2012) Neil D Young et al.   NATURE GENETICS

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda

(2012) Christopher W. Wheat et al.   SYSTEMATIC BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae)

(2011) Nicole E. White et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei

(2011) Andrea B. Kohn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level

(2011) Manuela Krüger et al.   NEW PHYTOLOGIST

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

(2011) Patrick Kück et al.   PLoS One

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

(2010) Alexander Keller et al.   Biology Direct

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

The Impact of rRNA Secondary Structure Consideration in Alignment and Tree Reconstruction: Simulated Data and a Case Study on the Phylogeny of Hexapods

(2010) Harald O. Letsch et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Dinoflagellate Phylogeny as Inferred from Heat Shock Protein 90 and Ribosomal Gene Sequences

(2010) Mona Hoppenrath et al.   PLoS One

A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

(2010) O. Rota-Stabelli et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A Phylogenomic Approach to Resolve the Basal Pterygote Divergence

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

concatenator: sequence data matrices handling made easy

(2009) F. PINA-MARTINS et al.   Molecular Ecology Resources

Simultaneous alignment and folding of 28S rRNA sequences uncovers phylogenetic signal in structure variation

(2009) Harald O. Letsch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The long way to diversity – Phylogeny and evolution of the Heterobranchia (Mollusca: Gastropoda)

(2009) Angela Dinapoli et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

(2009) Roman R. Stocsits et al.   NUCLEIC ACIDS RESEARCH

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Phylogenomic evidence for multiple losses of flight in ratite birds

(2008) J. Harshman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA