Published in Genome Biol Evol on March 09, 2017
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol (2012) 40.23
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol (2000) 35.86
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (2014) 28.04
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol (2012) 11.97
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics (2003) 9.53
Mitochondrial evolution. Science (1999) 8.59
Animal mitochondrial genomes. Nucleic Acids Res (1999) 7.75
PhyloWidget: web-based visualizations for the tree of life. Bioinformatics (2008) 7.37
Gaps as characters in sequence-based phylogenetic analyses. Syst Biol (2000) 6.52
Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol (2012) 5.64
Reductive evolution of resident genomes. Trends Microbiol (1998) 4.38
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science (2002) 4.19
A phylogenomic approach to microbial evolution. Nucleic Acids Res (2001) 3.06
Late-Neoproterozoic deep-ocean oxygenation and the rise of animal life. Science (2006) 2.97
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev (2012) 2.65
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol (2010) 2.58
TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon. Bioinformatics (2000) 2.54
GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics (2003) 2.42
Crystal structure of the entire respiratory complex I. Nature (2013) 2.34
Why have organelles retained genomes? Trends Genet (1999) 2.26
Extreme divergence of mitochondrial DNA within species of pulmonate land snails. Proc Biol Sci (1996) 1.94
A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst Biol (2009) 1.94
The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol (2010) 1.92
The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B Biol Sci (2003) 1.83
Oxygen, ecology, and the Cambrian radiation of animals. Proc Natl Acad Sci U S A (2013) 1.80
The ATP synthase: the understood, the uncertain and the unknown. Biochem Soc Trans (2013) 1.78
The first metazoa living in permanently anoxic conditions. BMC Biol (2010) 1.74
Mitochondrial evolution. Cold Spring Harb Perspect Biol (2012) 1.64
Diversity and reductive evolution of mitochondria among microbial eukaryotes. Philos Trans R Soc Lond B Biol Sci (2010) 1.58
Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol Biol Evol (2005) 1.50
Cyanobacterial NDH-1 complexes: novel insights and remaining puzzles. Biochim Biophys Acta (2010) 1.49
Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci Rep (2011) 1.45
Mitochondrial cytochrome b: evolution and structure of the protein. Biochim Biophys Acta (1993) 1.44
A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the alpha-proteobacterial mitochondrial ancestor. Mol Biol Evol (2009) 1.41
Nematoda from the terrestrial deep subsurface of South Africa. Nature (2011) 1.37
The unusual system of doubly uniparental inheritance of mtDNA: isn't one enough? Trends Genet (2007) 1.35
Accounting for alignment uncertainty in phylogenomics. PLoS One (2012) 1.35
The extrachromosomal DNAs of apicomplexan parasites. Annu Rev Microbiol (1994) 1.32
OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucleic Acids Res (2003) 1.25
Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM. Proc Natl Acad Sci U S A (2012) 1.20
Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol (2008) 1.16
Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. Elife (2015) 1.12
Doubly uniparental inheritance: two mitochondrial genomes, one precious model for organelle DNA inheritance and evolution. DNA Cell Biol (2009) 1.08
Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships. BMC Evol Biol (2011) 1.06
Biosynthesis and physiology of coenzyme Q in bacteria. Biochim Biophys Acta (2014) 1.04
Mitochondrion-related organelles in eukaryotic protists. Annu Rev Microbiol (2010) 1.01
Why chloroplasts and mitochondria contain genomes. Comp Funct Genomics (2003) 1.00
The long way to diversity--phylogeny and evolution of the Heterobranchia (Mollusca: Gastropoda). Mol Phylogenet Evol (2009) 1.00
Extreme mtDNA divergences in a terrestrial slug (Gastropoda, Pulmonata, Arionidae): accelerated evolution, allopatric divergence and secondary contact. J Evol Biol (2005) 0.99
Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria. Proc Natl Acad Sci U S A (2015) 0.99
Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One (2014) 0.97
Lophotrochozoan mitochondrial genomes. Integr Comp Biol (2006) 0.97
Rhodoquinone and complex II of the electron transport chain in anaerobically functioning eukaryotes. J Biol Chem (1995) 0.95
A resourceful genome: updating the functional repertoire and evolutionary role of animal mitochondrial DNAs. Trends Genet (2014) 0.94
Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system. Genome Biol Evol (2013) 0.94
A comparative analysis of mitochondrial ORFans: new clues on their origin and role in species with doubly uniparental inheritance of mitochondria. Genome Biol Evol (2013) 0.91
Bacterial genome chimaerism and the origin of mitochondria. Can J Microbiol (2011) 0.89
Transcriptional mapping and RNA processing of the Plasmodium falciparum mitochondrial mRNAs. Mol Biochem Parasitol (2000) 0.89
Organic structural specificity and sites of coenzyme Q in succinoxidase and DPNH-oxidase systems. Arch Biochem Biophys (1968) 0.89
Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes. Mol Biol Evol (2006) 0.89
Structure and function of mitochondrial complex I. Biochim Biophys Acta (2016) 0.87
Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins. BMC Biol (2015) 0.87
Animal mitochondria, positive selection and cyto-nuclear coevolution: insights from pulmonates. PLoS One (2013) 0.87
Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. PLoS One (2014) 0.86
The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with conchifera. BMC Genomics (2013) 0.85
MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evol Biol (2014) 0.85
Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome. Comp Biochem Physiol Part D Genomics Proteomics (2012) 0.80
Low-oxygen waters limited habitable space for early animals. Nat Commun (2016) 0.79
Genome Analysis of Structure-Function Relationships in Respiratory Complex I, an Ancient Bioenergetic Enzyme. Genome Biol Evol (2015) 0.77
Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia. Genome Biol Evol (2016) 0.77
The challenge of proving the existence of metazoan life in permanently anoxic deep-sea sediments. BMC Biol (2016) 0.76
Ediacaran Marine Redox Heterogeneity and Early Animal Ecosystems. Sci Rep (2015) 0.76
Animals, anoxic environments, and reasons to go deep. BMC Biol (2016) 0.76
Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia. Genome Biol Evol (2016) 0.77