BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

(2016) John W. Davey et al.   G3-Genes Genomes Genetics

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

Genome Update. Let the consumer beware:Streptomycesgenome sequence quality

(2016) David J. Studholme   Microbial Biotechnology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A maturing understanding of the composition of the insect gene repertoire

(2015) Robert M Waterhouse   Current Opinion in Insect Science

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Finding the missing honey bee genes: lessons learned from a genome upgrade

(2014) Christine G Elsik et al.   BMC GENOMICS

Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers

(2014) Rosa Fernández et al.   CURRENT BIOLOGY

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

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

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

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

(2010) Robert M. Waterhouse et al.   Genome Biology and Evolution

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

(2009) Shani Blanga-Kanfi et al.   BMC EVOLUTIONARY BIOLOGY