Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing

(2012) Dick SJ Groenenberg et al.   BMC GENOMICS

Next-generation sequencing and large genome assemblies

(2012) Joseph Henson et al.   PHARMACOGENOMICS

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

(2012) Agnes Dettai et al.   PLoS One

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

(2011) Paolo D'Onorio de Meo et al.   NUCLEIC ACIDS RESEARCH

Global Diversity of Ascidiacea

(2011) Noa Shenkar et al.   PLoS One

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Index-Free De Novo Assembly and Deconvolution of Mixed Mitochondrial Genomes

(2010) B. J. McComish et al.   Genome Biology and Evolution

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

(2010) Georgia Tsagkogeorga et al.   JOURNAL OF MOLECULAR EVOLUTION

A molecular phylogeny of the Thaliacea

(2010) A. F. Govindarajan et al.   JOURNAL OF PLANKTON RESEARCH

Erosion of phylogenetic signal in tunicate mitochondrial genomes on different levels of analysis

(2010) Thomas Stach et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

(2010) M. J. T. N. Timmermans et al.   NUCLEIC ACIDS RESEARCH

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

(2010) F. Denoeud et al.   SCIENCE

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

Genetic Perspectives on Marine Biological Invasions

(2009) Jonathan B. Geller et al.   Annual Review of Marine Science

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

(2009) Georgia Tsagkogeorga et al.   BMC EVOLUTIONARY BIOLOGY

Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

(2009) Tiratha Singh et al.   BMC GENOMICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Hypervariability of Ascidian Mitochondrial Gene Order: Exposing the Myth of Deuterostome Organelle Genome Stability

(2009) Carmela Gissi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Refining the Ciona intestinalis Model of Central Nervous System Regeneration

(2009) Carl Dahlberg et al.   PLoS One

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

The solitary ascidian Herdmania momus: native (Red Sea) versus non-indigenous (Mediterranean) populations

(2008) N. Shenkar et al.   BIOLOGICAL INVASIONS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The complete mitochondrial genome of the demosponge Negombata magnifica (Poecilosclerida)

(2008) Frida Belinky et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences

(2008) R. Pérez-Portela et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION