Drivers and dynamics of a massive adaptive radiation in cichlid fishes

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

The genomic timeline of cichlid fish diversification across continents

(2020) Michael Matschiner et al.   Nature Communications

Repeated evolution vs common ancestry: Sex chromosome evolution in the haplochromine cichlid Pseudocrenilabrus philander

(2019) Astrid Böhne et al.   Genome Biology and Evolution

East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation

(2019) Frederic Dieter Benedikt Schedel et al.   BMC EVOLUTIONARY BIOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

The taxonomic diversity of the cichlid fish fauna of ancient Lake Tanganyika, East Africa

(2019) Fabrizia Ronco et al.   JOURNAL OF GREAT LAKES RESEARCH

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Understanding explosive diversification through cichlid fish genomics

(2018) Walter Salzburger   NATURE REVIEWS GENETICS

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

(2018) Iker Irisarri et al.   Nature Communications

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

(2018) Milan Malinsky et al.   Nature Ecology & Evolution

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

(2017) Huw A. Ogilvie et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mega-evolutionary dynamics of the adaptive radiation of birds

(2017) Christopher R. Cooney et al.   NATURE

Speciation gradients and the distribution of biodiversity

(2017) Dolph Schluter et al.   NATURE

Ancient hybridization fuels rapid cichlid fish adaptive radiations

(2017) Joana I. Meier et al.   Nature Communications

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

(2017) Martin Malmstrøm et al.   Scientific Data

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

The genomics of organismal diversification illuminated by adaptive radiations

(2015) Daniel Berner et al.   TRENDS IN GENETICS

Ecology and Evolution of the African Great Lakes and Their Faunas

(2014) Walter Salzburger et al.   Annual Review of Ecology Evolution and Systematics

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

geomorph: anrpackage for the collection and analysis of geometric morphometric shape data

(2013) Dean C. Adams et al.   Methods in Ecology and Evolution

Convergent Evolution within an Adaptive Radiation of Cichlid Fishes

(2012) Moritz Muschick et al.   CURRENT BIOLOGY

TINA manual landmarking tool: software for the precise digitization of 3D landmarks

(2012) Anja C Schunke et al.   Frontiers in Zoology

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Multiple routes to mammalian diversity

(2011) Chris Venditti et al.   NATURE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Phylogenetic Insights on Adaptive Radiation

(2010) Richard E. Glor   Annual Review of Ecology Evolution and Systematics

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adaptive Radiation: Contrasting Theory with Data

(2009) S. Gavrilets et al.   SCIENCE

The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes

(2008) WALTER SALZBURGER   MOLECULAR ECOLOGY