Annotation and analysis of the mitochondrial genome of Coniothyrium glycines, causal agent of red leaf blotch of soybean, reveals an abundance of homing endonucleases

Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Shiraia bambusicola Reveals Special Features in the Order of Pleosporales

(2015) Xiao-Ye Shen et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Automated ensemble assembly and validation of microbial genomes

(2014) Sergey Koren et al.   BMC BIOINFORMATICS

Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogenRhizoctonia solaniAG-3

(2014) Liliana Losada et al.   FEMS MICROBIOLOGY LETTERS

High Variability of Mitochondrial Gene Order among Fungi

(2014) Gabriela Aguileta et al.   Genome Biology and Evolution

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

(2014) Andrey V. Mardanov et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

(2013) Timothy Y. James et al.   CURRENT BIOLOGY

Sizing up Septoria

(2013) W. Quaedvlieg et al.   STUDIES IN MYCOLOGY

Redisposition of phoma-like anamorphs in Pleosporales

(2013) J. de Gruyter et al.   STUDIES IN MYCOLOGY

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

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

Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae

(2010) Christine L. Stone et al.   MYCOLOGIA

The Agaricus bisporus cox1 Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns

(2010) Cyril Férandon et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genes within Genes: Multiple LAGLIDADG Homing Endonucleases Target the Ribosomal Protein S3 Gene Encoded within an rnl Group I Intron of Ophiostoma and Related Taxa

(2009) J. Sethuraman et al.   MOLECULAR BIOLOGY AND EVOLUTION

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The mitochondrial genome of the Basidiomycete fungusPleurotus ostreatus(oyster mushroom)

(2008) Yong Wang et al.   FEMS MICROBIOLOGY LETTERS

Frequent, Phylogenetically Local Horizontal Transfer of the cox1 Group I Intron in Flowering Plant Mitochondria

(2008) M. V. Sanchez-Puerta et al.   MOLECULAR BIOLOGY AND EVOLUTION

The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109kb in size and contains a stable integrated plasmid

(2008) Eduardo F. Formighieri et al.  

Reevaluation of the cox1 Group I Intron in Araceae and Angiosperms Indicates a History Dominated by Loss rather than Horizontal Transfer

(2007) N. Cusimano et al.   MOLECULAR BIOLOGY AND EVOLUTION