A genome-scale phylogeny of the kingdom Fungi
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Jacob L. Steenwyk | J. Stajich | A. Rokas | J. Spatafora | T. James | C. T. Hittinger | M. Groenewald | J. Steenwyk | Yuanning Li | C. Dunn | Yan Wang | Ying Chang | Xing‐Xing Shen
[1] A. Rokas,et al. An investigation of irreproducibility in maximum likelihood phylogenetic inference , 2020, Nature Communications.
[2] D. Moreira,et al. Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota , 2020, Nature Communications.
[3] A. Rokas,et al. Rooting the Animal Tree of Life , 2020, bioRxiv.
[4] A. Salamov,et al. Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi , 2020, Scientific Reports.
[5] J. Stajich,et al. Toward a Fully Resolved Fungal Tree of Life. , 2020, Annual review of microbiology.
[6] Yuanning Li,et al. Feature frequency profile-based phylogenies are inaccurate , 2020, Proceedings of the National Academy of Sciences.
[7] Jacob L. Steenwyk,et al. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota , 2020, Science Advances.
[8] Javier F. Tabima,et al. Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus , 2020, bioRxiv.
[9] Donovan H. Parks,et al. Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy , 2020, bioRxiv.
[10] A. Salamov,et al. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens , 2020, Studies in mycology.
[11] Olga Chernomor,et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.
[12] Stephen A. Smith,et al. PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS. , 2019, Systematic biology.
[13] P. Kirk,et al. Notes, outline and divergence times of Basidiomycota , 2019, Fungal Diversity.
[14] M. C. Aime,et al. Model Choice, Missing Data and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships. , 2019, Systematic biology.
[15] J. Stajich,et al. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). , 2019, Molecular phylogenetics and evolution.
[16] P. Bork,et al. Interactive Tree Of Life (iTOL) v4: recent updates and new developments , 2019, Nucleic Acids Res..
[17] J. Ruiz-Herrera,et al. Cell wall glucans of fungi. A review , 2019, Cell surface.
[18] L. Nagy,et al. Comparative genomics reveals the origin of fungal hyphae and multicellularity , 2019, Nature Communications.
[19] Anna Lipzen,et al. Megaphylogeny resolves global patterns of mushroom evolution , 2019, Nature Ecology & Evolution.
[20] D. Hibbett,et al. Contemporaneous radiations of fungi and plants linked to symbiosis , 2018, Nature Communications.
[21] D. Moreira,et al. Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi , 2018, Communications Biology.
[22] Moriya Ohkuma,et al. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum , 2018, Cell.
[23] Donovan H. Parks,et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life , 2018, Nature Biotechnology.
[24] Emmanuel Paradis,et al. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..
[25] Jacob L. Steenwyk,et al. A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium , 2018, mBio.
[26] Kessy Abarenkov,et al. High-level classification of the Fungi and a tool for evolutionary ecological analyses , 2018, Fungal Diversity.
[27] Chao Zhang,et al. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees , 2018, BMC Bioinformatics.
[28] G. Torruella,et al. Clarifying the Relationships between Microsporidia and Cryptomycota , 2018, The Journal of eukaryotic microbiology.
[29] A. Salamov,et al. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species , 2018, Proceedings of the National Academy of Sciences.
[30] T. James,et al. The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism , 2017, eLife.
[31] Joseph Heitman,et al. The Fungal Kingdom , 2017 .
[32] T. James,et al. Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life. , 2017, Annual review of microbiology.
[33] J. Stajich,et al. The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. , 2017, Microbiology spectrum.
[34] Siavash Mirarab,et al. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies , 2017, Genes.
[35] Robert M. Waterhouse,et al. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.
[36] Sung-Hou Kim,et al. A genome Tree of Life for the Fungi kingdom , 2017, Proceedings of the National Academy of Sciences.
[37] Robert Lücking,et al. Fungal Diversity Revisited: 2.2 to 3.8 Million Species , 2017, Microbiology spectrum.
[38] A. von Haeseler,et al. UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.
[39] Antonis Rokas,et al. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets , 2017, bioRxiv.
[40] K. Hyde,et al. A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective , 2017, Fungal Diversity.
[41] Thomas K. F. Wong,et al. ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.
[42] A. Rokas,et al. Contentious relationships in phylogenomic studies can be driven by a handful of genes , 2017, Nature Ecology &Evolution.
[43] Evgeny M. Zdobnov,et al. OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs , 2016, Nucleic Acids Res..
[44] D. Weese,et al. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error , 2016, Systematic biology.
[45] J. Stajich,et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data , 2016, Mycologia.
[46] Antonis Rokas,et al. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data , 2016, G3: Genes, Genomes, Genetics.
[47] Sudhir Kumar,et al. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.
[48] T. Jeffries,et al. Genomics and the making of yeast biodiversity. , 2015, Current opinion in genetics & development.
[49] A. Roger,et al. Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi , 2015, Current Biology.
[50] M. Berbee,et al. Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi , 2015, Mycologia.
[51] A. Salamov,et al. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants , 2015, Genome biology and evolution.
[52] L. Moroz,et al. Error, signal, and the placement of Ctenophora sister to all other animals , 2015, Proceedings of the National Academy of Sciences.
[53] John Gatesy,et al. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. , 2014, Molecular phylogenetics and evolution.
[54] Tandy J. Warnow,et al. ASTRAL: genome-scale coalescent-based species tree estimation , 2014, Bioinform..
[55] Alexandros Stamatakis,et al. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. , 2014, Molecular biology and evolution.
[56] D. Forsdyke. Evolutionary Bioinformatics , 2006, Springer International Publishing.
[57] Inna Dubchak,et al. MycoCosm portal: gearing up for 1000 fungal genomes , 2013, Nucleic Acids Res..
[58] C. Gostinčar,et al. Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent , 2013, BMC Genomics.
[59] J. Stajich,et al. Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia , 2013, Current Biology.
[60] Antonis Rokas,et al. Inferring ancient divergences requires genes with strong phylogenetic signals , 2013, Nature.
[61] R. Humber,et al. Phylogenetic lineages in Entomophthoromycota , 2013, Persoonia.
[62] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[63] Alexandros Stamatakis,et al. Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice , 2012, Systematic biology.
[64] T. Gabaldón,et al. Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi , 2012, BMC Biology.
[65] D. Hibbett,et al. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. , 2012, Fungal genetics and biology : FG & B.
[66] B. Lang,et al. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. , 2012, Molecular biology and evolution.
[67] A. von Haeseler,et al. A Consistent Phylogenetic Backbone for the Fungi , 2011, Molecular biology and evolution.
[68] M. Berbee,et al. A multigene phylogeny of Olpidium and its implications for early fungal evolution , 2011, BMC Evolutionary Biology.
[69] M. Blackwell. The fungi: 1, 2, 3 ... 5.1 million species? , 2011, American journal of botany.
[70] Matthew W. Brown,et al. Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. , 2009, Molecular biology and evolution.
[71] B. Lang,et al. Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support , 2009, BMC Evolutionary Biology.
[72] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[73] O. Gascuel,et al. Phylogenetic mixture models for proteins , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.
[74] G. Purschke,et al. Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa). , 2008, Molecular phylogenetics and evolution.
[75] Michael Weiss,et al. A higher-level phylogenetic classification of the Fungi. , 2007, Mycological research.
[76] R. Agarwala,et al. Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST , 2006, BMC Biology.
[77] Kenji Matsuura,et al. Reconstructing the early evolution of Fungi using a six-gene phylogeny , 2006, Nature.
[78] Burkhard Morgenstern,et al. AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..
[79] S. Carroll,et al. Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.
[80] Zemin Zhang,et al. A profile hidden Markov model for signal peptides generated by HMMER , 2003, Bioinform..
[81] Daniel Schwarzott,et al. A new fungal phylum, the Glomeromycota: phylogeny and evolution * * Dedicated to Manfred Kluge (Tech , 2001 .
[82] G. C. Johns,et al. Proposal for a standardized temporal scheme of biological classification for extant species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[83] J. Felsenstein. Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .
[84] J. K. Liu,et al. Outline of Fungi and fungus-like taxa , 2020 .
[85] Scott V Edwards,et al. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. , 2016, Molecular phylogenetics and evolution.