A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

(2017) Prosanta Chakrabarty et al.   SYSTEMATIC BIOLOGY

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

(2017) Matthew A. Campbell et al.   PeerJ

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses

(2016) Juan Marcos Mirande   CLADISTICS

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms

(2016) Hao Yuan et al.   Molecular Ecology Resources

Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia

(2015) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selecting informative subsets of sparse supermatrices increases the chance to find correct trees

(2013) Bernhard Misof et al.   BMC BIOINFORMATICS

EVOLUTIONARY ORIGIN AND EARLY BIOGEOGRAPHY OF OTOPHYSAN FISHES (OSTARIOPHYSI: TELEOSTEI)

(2013) Wei-Jen Chen et al.   EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

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

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

(2011) Masanori Nakatani et al.   BMC EVOLUTIONARY BIOLOGY

Marine dispersal as a pre-requisite for Gondwanan vicariance among elements of the galaxiid fish fauna

(2011) Christopher P. Burridge et al.   JOURNAL OF BIOGEOGRAPHY

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes

(2010) Chenhong Li et al.   BMC EVOLUTIONARY BIOLOGY

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes

(2010) Jun Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Higher and lower-level relationships of the deep-sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences

(2009) JAN Y. POULSEN et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The phylogenetic position of an undescribed paedomorphic clupeiform taxon: mitogenomic evidence

(2008) Sébastien Lavoué et al.   ICHTHYOLOGICAL RESEARCH

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

(2008) Sébastien Lavoué et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION