The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

(2016) Kirill V. Mikhailov et al.   CURRENT BIOLOGY

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

(2015) Christopher E. Laumer et al.   CURRENT BIOLOGY

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics

(2015) Gonzalo Giribet   ORGANISMS DIVERSITY & EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Patrick Kück et al.   Frontiers in Zoology

Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

(2014) Torsten H. Struck et al.   MOLECULAR BIOLOGY AND EVOLUTION

What helminth genomes have taught us about parasite evolution

(2014) MAGDALENA ZAROWIECKI et al.   PARASITOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

BMP and Delta/Notch signaling control the development of amphioxus epidermal sensory neurons: insights into the evolution of the peripheral sensory system

(2012) T.-M. Lu et al.   DEVELOPMENT

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Distinction of Cell Types in Dicyema japonicum (Phylum Dicyemida) by Expression Patterns of 16 Genes

(2011) Kazutoyo Ogino et al.   JOURNAL OF PARASITOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

(2011) Carla A. Cummins et al.   SYSTEMATIC 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

Phylogenetic Analysis of Dicyemid Mesozoans (Phylum Dicyemida) From Innexin Amino Acid Sequences: Dicyemids Are Not Related to Platyhelminthes

(2010) Takahito G. Suzuki et al.   JOURNAL OF PARASITOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY