Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

A family-level Tree of Life for bivalves based on a Sanger-sequencing approach

(2017) David J. Combosch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New Cytotoxic Norditerpenes from the Australian Nudibranchs Goniobranchus Splendidus and Goniobranchus Daphne

(2016) Yuichiro Hirayama et al.   AUSTRALIAN JOURNAL OF CHEMISTRY

Dating and biogeographical patterns in the sea slug genus Acanthodoris Gray, 1850 (Mollusca, Gastropoda, Nudibranchia)

(2016) Joshua M. Hallas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex

(2016) Vinicius Padula et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diaphorodoris alba Portmann & Sandmeier, 1960 is a valid species: molecular and morphological comparison with D. luteocincta (M. Sars, 1870) (Gastropoda: Nudibranchia)

(2016) GIULIA FURFARO et al.   ZOOTAXA

Coloration and Defense in the Nudibranch Gastropod Hypselodoris fontandraui

(2016) Markus Haber et al.   BIOLOGICAL BULLETIN

Color Pattern Variation in a Shallow-Water Species of Opisthobranch Mollusc

(2016) Ángel Valdés et al.   BIOLOGICAL BULLETIN

The Model Organism Hermissenda crassicornis (Gastropoda: Heterobranchia) Is a Species Complex

(2016) Tabitha Lindsay et al.   PLoS One

A Radical Solution: The Phylogeny of the Nudibranch Family Fionidae

(2016) Kristen Cella et al.   PLoS One

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

(2015) David A. Morrison et al.   AUSTRALIAN SYSTEMATIC BOTANY

Molecular evaluation of the phylogenetic position of the enigmatic species Trivettea papalotla (Bertsch) (Mollusca : Nudibranchia)

(2015) Ryan E. Hulett et al.   INVERTEBRATE SYSTEMATICS

Family matters: The first molecular phylogeny of the Onchidorididae Gray, 1827 (Mollusca, Gastropoda, Nudibranchia)

(2015) Joshua M. Hallas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Is Sequence Alignment an Art or a Science?

(2015) David A. Morrison   SYSTEMATIC BOTANY

Seeing double: pseudocryptic diversity in theDoriopsilla albopunctata-Doriopsilla gemelaspecies complex of the north-eastern Pacific

(2015) Craig Hoover et al.   ZOOLOGICA SCRIPTA

Molecular and morphological systematics of Doto Oken, 1851 (Gastropoda: Heterobranchia), with descriptions of five new species and a new genus

(2015) CARISSA SHIPMAN et al.   ZOOTAXA

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation

(2015) Jessica A. Goodheart et al.   Royal Society Open Science

Molecular and morphological systematics of neustonic nudibranchs (Mollusca : Gastropoda : Glaucidae : Glaucus), with descriptions of three new cryptic species

(2014) Celia K. C. Churchill et al.   INVERTEBRATE SYSTEMATICS

Identification of five species of Dendrodoris (Mollusca: Nudibranchia) from Japan, using DNA barcode and larval characters

(2014) Mamiko Hirose et al.   Marine Biodiversity

Population Biology of an Intertidal Dorid Nudibranch (Onchidoris muricata) in the Southern Gulf of Maine, U.S.A.: Changes in Phenology Due to an Invasive Prey?

(2013) Walter J. Lambert   AMERICAN MALACOLOGICAL BULLETIN

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

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

Phylogenomics supports Panpulmonata: Opisthobranch paraphyly and key evolutionary steps in a major radiation of gastropod molluscs

(2013) Kevin M. Kocot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Flashback and foreshadowing—a review of the taxon Opisthobranchia

(2013) Heike Wägele et al.   ORGANISMS DIVERSITY & EVOLUTION

Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results

(2013) Pilar Suñé et al.   PLoS One

A Tale That Morphology Fails to Tell: A Molecular Phylogeny of Aeolidiidae (Aeolidida, Nudibranchia, Gastropoda)

(2013) Leila Carmona et al.   PLoS One

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Traditional Taxonomic Groupings Mask Evolutionary History: A Molecular Phylogeny and New Classification of the Chromodorid Nudibranchs

(2012) Rebecca Fay Johnson et al.   PLoS One

PhyDesign: an online application for profiling phylogenetic informativeness

(2011) Francesc López-Giráldez et al.   BMC EVOLUTIONARY BIOLOGY

3D-anatomy of a new tropical Peruvian nudibranch gastropod species, Corambe mancorensis, and novel hypotheses on dorid gill ontogeny and evolution

(2011) Alexander Martynov et al.   JOURNAL OF MOLLUSCAN STUDIES

Crawling through time: Transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomics

(2011) Mónica Medina et al.   Marine Genomics

Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates

(2011) Andrew H. Moeller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny and evolution of corambid nudibranchs (Mollusca: Gastropoda)

(2011) ALEXANDER MARTYNOV et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Phylogenetic analysis of Dendronotus nudibranchs with emphasis on northeastern Pacific species

(2010) C. C. Stout et al.   JOURNAL OF MOLLUSCAN STUDIES

Inference of molecular homology and sequence alignment by direct optimization

(2010) Matthew J. Morgan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The first molecular phylogeny of cladobranchian opisthobranchs (Mollusca, Gastropoda, Nudibranchia)

(2010) Marta Pola et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

Out of Antarctica? – New insights into the phylogeny and biogeography of the Pleurobranchomorpha (Mollusca, Gastropoda)

(2009) Katrin Göbbeler 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

Why Would Phylogeneticists Ignore Computerized Sequence Alignment?

(2009) David A. Morrison   SYSTEMATIC BIOLOGY