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Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships

https://doi.org/10.1101/170696
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inferredcites →https://doi.org/10.1007/s00239-011-9461-4openalex-snapshot
Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom
inferredcites →https://doi.org/10.1007/s11557-006-0502-0openalex-snapshot
The simple-septate basidiomycetes: a synopsis
inferredcites →https://doi.org/10.1016/j.cub.2012.05.018openalex-snapshot
Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera
inferredcites →https://doi.org/10.1016/j.cub.2015.07.060openalex-snapshot
Phylogenomic Insights into Animal Evolution
inferredcites →https://doi.org/10.1016/j.fgb.2006.05.001openalex-snapshot
A phylogenomic analysis of the Ascomycota
inferredcites →https://doi.org/10.1016/j.fgb.2012.01.007openalex-snapshot
The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction
inferredcites →https://doi.org/10.1016/j.mycres.2007.03.004openalex-snapshot
A higher-level phylogenetic classification of the Fungi
inferredcites →https://doi.org/10.1016/j.tig.2006.02.003openalex-snapshot
Phylogenomics: the beginning of incongruence?
inferredcites →https://doi.org/10.1016/j.tpb.2014.12.005openalex-snapshot
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
inferredcites →https://doi.org/10.1016/j.tplants.2004.08.008openalex-snapshot
Genome-scale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics
inferredcites →https://doi.org/10.1016/j.ympev.2006.08.024openalex-snapshot
Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)
inferredcites →https://doi.org/10.1038/425782aopenalex-snapshot
Ending incongruence
inferredcites →https://doi.org/10.1038/nature02053openalex-snapshot
Genome-scale approaches to resolving incongruence in molecular phylogenies
inferredcites →https://doi.org/10.1038/nature05110openalex-snapshot
Reconstructing the early evolution of Fungi using a six-gene phylogeny
inferredcites →https://doi.org/10.1038/nature06614openalex-snapshot
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inferredcites →https://doi.org/10.1038/nature10526openalex-snapshot
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inferredcites →https://doi.org/10.1038/nature15697openalex-snapshot
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inferredcites →https://doi.org/10.1038/nature19417openalex-snapshot
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inferredcites →https://doi.org/10.1038/ncomms14444openalex-snapshot
Innovation and constraint leading to complex multicellularity in the Ascomycota
inferredcites →https://doi.org/10.1038/ncomms5471openalex-snapshot
Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
inferredcites →https://doi.org/10.1038/ng.3223openalex-snapshot
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
inferredcites →https://doi.org/10.1038/nrg1603openalex-snapshot
Phylogenomics and the reconstruction of the tree of life
inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot
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inferredcites →https://doi.org/10.1073/pnas.1202997109openalex-snapshot
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
inferredcites →https://doi.org/10.1073/pnas.1400592111openalex-snapshot
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
inferredcites →https://doi.org/10.1073/pnas.1503453112openalex-snapshot
Error, signal, and the placement of Ctenophora sister to all other animals
inferredcites →https://doi.org/10.1073/pnas.1518127112openalex-snapshot
Genomic data do not support comb jellies as the sister group to all other animals
inferredcites →https://doi.org/10.1073/pnas.94.13.6815openalex-snapshot
Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
inferredcites →https://doi.org/10.1080/00275514.1993.12026354openalex-snapshot
Higher Taxa of Basidiomycetes: An 18S Rrna Gene Perspective
inferredcites →https://doi.org/10.1080/00275514.1995.12026603openalex-snapshot
Phylogenetic Relationships in Auriculariaceous Basidiomycetes Based on 25S Ribosomal DNA Sequences
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1080/10635150701397643openalex-snapshot
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
inferredcites →https://doi.org/10.1080/10635150802306527openalex-snapshot
Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies
inferredcites →https://doi.org/10.1093/bib/bbr030openalex-snapshot
Computational methods for Gene Orthology inference
inferredcites →https://doi.org/10.1093/bioinformatics/17.12.1246openalex-snapshot
CONSEL: for assessing the confidence of phylogenetic tree selection
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.502openalex-snapshot
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot
phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/gbe/evs104openalex-snapshot
Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data
inferredcites →https://doi.org/10.1093/molbev/msh137openalex-snapshot
Genome-Scale Phylogeny and the Detection of Systematic Biases
inferredcites →https://doi.org/10.1093/molbev/msq166openalex-snapshot
Mammalian Evolution May not Be Strictly Bifurcating
inferredcites →https://doi.org/10.1093/molbev/msr202openalex-snapshot
Statistics and Truth in Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msr285openalex-snapshot
A Consistent Phylogenetic Backbone for the Fungi
inferredcites →https://doi.org/10.1093/molbev/mst196openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msu235openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msu245openalex-snapshot
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msv258openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msv266openalex-snapshot
The Impact of Missing Data on Species Tree Estimation
inferredcites →https://doi.org/10.1093/molbev/msv337openalex-snapshot
Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
inferredcites →https://doi.org/10.1093/molbev/msv347openalex-snapshot
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
inferredcites →https://doi.org/10.1093/nar/gkt1183openalex-snapshot
MycoCosm portal: gearing up for 1000 fungal genomes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/syr064openalex-snapshot
A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases
inferredcites →https://doi.org/10.1093/sysbio/syt022openalex-snapshot
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
inferredcites →https://doi.org/10.1093/sysbio/syt023openalex-snapshot
Anomalous Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syu063openalex-snapshot
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syv016openalex-snapshot
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
inferredcites →https://doi.org/10.1093/sysbio/syv058openalex-snapshot
How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards
inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/syw079openalex-snapshot
Phylogenomics of Lophotrochozoa with Consideration of Systematic Error
inferredcites →https://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferredcites →https://doi.org/10.1098/rspb.2009.0896openalex-snapshot
Assessing the root of bilaterian animals with scalable phylogenomic methods
inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1098/rstb.2008.0144openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.186668.114openalex-snapshot
Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
inferredcites →https://doi.org/10.1111/nph.12653openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.1158395openalex-snapshot
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
inferredcites →https://doi.org/10.1126/science.1221748openalex-snapshot
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1146/annurev.ecolsys.35.112202.130205openalex-snapshot
Phylogenomics
inferredcites →https://doi.org/10.1186/1471-2105-14-348openalex-snapshot
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees
inferredcites →https://doi.org/10.1186/1471-2148-12-100openalex-snapshot
Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)
inferredcites →https://doi.org/10.1186/1471-2148-14-82openalex-snapshot
Selecting optimal partitioning schemes for phylogenomic datasets
inferredcites →https://doi.org/10.1186/1471-2148-6-99openalex-snapshot
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
inferredcites →https://doi.org/10.1186/1471-2164-14-617openalex-snapshot
Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
inferredcites →https://doi.org/10.1186/gb-2008-9-10-235openalex-snapshot
Large-scale assignment of orthology: back to phylogenetics?
inferredcites →https://doi.org/10.1186/s12862-015-0423-0openalex-snapshot
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
inferredcites →https://doi.org/10.1186/s12864-015-1380-0openalex-snapshot
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inferredcites →https://doi.org/10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7openalex-snapshot
Concatenation Analyses in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.3732/ajb.91.10.1446openalex-snapshot
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits
inferredcites →https://doi.org/10.3852/13-196openalex-snapshot
Toward genome-enabled mycology
inferredcites →https://doi.org/10.3852/mycologia.98.6.896openalex-snapshot
An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences
inferredcites →https://doi.org/10.3852/mycologia.98.6.917openalex-snapshot
A phylogenetic overview of the Agaricomycotina
inferredcites →https://doi.org/10.4137/ebo.s12813openalex-snapshot
PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
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