A masculinizing supergene underlies an exaggerated male reproductive morph in a spider

Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms

(2021) Paul Jay et al.   NATURE GENETICS

Lep-Anchor: automated construction of linkage map anchored haploid genomes

(2020) Pasi Rastas   BIOINFORMATICS

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Phylogenetic analysis and embryonic expression of panarthropod Dmrt genes

(2019) Virginia Panara et al.   Frontiers in Zoology

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Candidate genes associated with color morphs of female-limited polymorphisms of the damselfly Ischnura senegalensis

(2018) Michihiko Takahashi et al.   HEREDITY

Invertebrate acetylcholinesterases: Insights into their evolution and non-classical functions

(2018) Young Ho Kim et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Invertebrate acetylcholinesterases: Insights into their evolution and non-classical functions

(2018) Young Ho Kim et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

Selection for costly sexual traits results in a vacant mating niche and male dimorphism

(2015) Frederik Hendrickx et al.   EVOLUTION

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2Recombinant Crosses as an Example

(2015) Pasi Rastas et al.   Genome Biology and Evolution

The locus of sexual selection: moving sexual selection studies into the post-genomics era

(2015) G. S. Wilkinson et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly

(2015) Hideki Nishikawa et al.   NATURE GENETICS

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

Pan-metazoan phylogeny of the DMRT gene family: a framework for functional studies

(2014) Judith R. Wexler et al.   DEVELOPMENT GENES AND EVOLUTION

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A general approach to power calculation for relationship testing

(2013) Thore Egeland et al.   Forensic Science International-Genetics

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

Sex and the singular DM domain: insights into sexual regulation, evolution and plasticity

(2012) Clinton K. Matson et al.   NATURE REVIEWS GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Diversification of doublesex function underlies morph-, sex-, and species-specific development of beetle horns

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

Dmrt genes in the development and evolution of sexual dimorphism

(2012) Artyom Kopp   TRENDS IN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Cephalic modifications in dimorphic dwarf spiders of the genus oedothorax (Erigoninae, Linyphiidae, Araneae) and their evolutionary implications

(2011) Peter Michalik et al.   JOURNAL OF MORPHOLOGY

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One