Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Magic-BLAST, an accurate RNA-seq aligner for long and short reads

(2019) Grzegorz M. Boratyn et al.   BMC BIOINFORMATICS

The complete coding region of the maxicircle as a superior phylogenetic marker for exploring evolutionary relationships between members of the Leishmaniinae

(2019) Alexa Kaufer et al.   INFECTION GENETICS AND EVOLUTION

FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

(2018) Kathrin M Seibt et al.   BIOINFORMATICS

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum

(2017) Bart Cuypers et al.   Genome Biology and Evolution

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

(2017) Sergey Koren et al.   GENOME RESEARCH

History of the fragmentation of the African rain forest in the Dahomey Gap: insight from the demographic history of Terminalia superba

(2017) Boris B. Demenou et al.   HEREDITY

Discovery and genomic analyses of hybridization between divergent lineages of Trypanosoma congolense , causative agent of Animal African Trypanosomiasis

(2017) Eliane Tihon et al.   MOLECULAR ECOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

NOVOPlasty:de novoassembly of organelle genomes from whole genome data

(2016) Nicolas Dierckxsens et al.   NUCLEIC ACIDS RESEARCH

Population genomics reveals the origin and asexual evolution of human infective trypanosomes

(2016) William Weir et al.   eLife

MeDuSa: a multi-draft based scaffolder

(2015) Emanuele Bosi et al.   BIOINFORMATICS

Kinetoplast adaptations in American strains from Trypanosoma vivax

(2015) Gonzalo Greif et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

(2015) Martyna Molak et al.   PeerJ

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

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

A draft genome for the African crocodilian trypanosome Trypanosoma grayi

(2014) Steven Kelly et al.   Scientific Data

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Network News: The Replication of Kinetoplast DNA

(2012) Robert E. Jensen et al.   Annual Review of Microbiology

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Scarce events of mitochondrial introgression in Trypanosoma cruzi: New case with a Bolivian strain

(2012) Christian Barnabé et al.   INFECTION GENETICS AND EVOLUTION

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing

(2012) Louisa A. Messenger et al.   PLoS Neglected Tropical Diseases

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Phylogeography and Taxonomy of Trypanosoma brucei

(2011) Oliver Balmer et al.   PLoS Neglected Tropical Diseases

Recent, Independent and Anthropogenic Origins of Trypanosoma cruzi Hybrids

(2011) Michael D. Lewis et al.   PLoS Neglected Tropical Diseases

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic analysis reveals the presence of the Trypanosoma cruzi clade in African terrestrial mammals☆

(2008) P HAMILTON et al.   INFECTION GENETICS AND EVOLUTION

Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei

(2008) D.-H. Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA