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Prospects for Building the Tree of Life from Large Sequence Databases
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1098-2418(199903)14:2<153::aid-rsa3>3.0.co;2-ropenalex-snapshot
A few logs suffice to build (almost) all trees (I)
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Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny
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Phylogenetic supertrees: Assembling the trees of life
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18S gene trees are positively misleading for monocot/dicot phylogenetics
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The challenge of constructing large phylogenetic trees
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba
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inferredcites →https://doi.org/10.1080/106351598261067openalex-snapshot
On the Best Evolutionary Rate for Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btg1000openalex-snapshot
Bayesian gene/species tree reconciliation and orthology analysis using MCMC
inferredcites →https://doi.org/10.1093/molbev/msg115openalex-snapshot
Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases
inferredcites →https://doi.org/10.1093/molbev/msh182openalex-snapshot
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025950openalex-snapshot
Searching for the Closest Living Relative(s) of Tetrapods Through Evolutionary Analysis of Mitochondrial and Nuclear Data
inferredcites →https://doi.org/10.1093/sysbio/45.3.363openalex-snapshot
General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa
inferredcites →https://doi.org/10.1111/j.1095-8312.1981.tb01847.xopenalex-snapshot
A likelihood approach to character weighting and what it tells us about parsimony and compatibility
inferredcites →https://doi.org/10.1371/journal.pbio.0000019openalex-snapshot
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria
inferredcites →https://doi.org/10.2307/2399952openalex-snapshot
Angiosperm Phylogeny Inferred from 18S Ribosomal DNA Sequences
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics
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A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses
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An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree
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Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia
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Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci
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High-resolution species trees without concatenation
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Supertree Bootstrapping Methods for Assessing Phylogenetic Variation among Genes in Genome-Scale Data Sets
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SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics
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Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees
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inferred← citeshttps://doi.org/10.1093/sysbio/syu038openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syv058openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syw057openalex-snapshot
The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes
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inferred← citeshttps://doi.org/10.1093/sysbio/syw102openalex-snapshot
Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles
inferred← citeshttps://doi.org/10.1093/sysbio/syx077openalex-snapshot
To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
inferred← citeshttps://doi.org/10.1093/sysbio/syz058openalex-snapshot
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlab108openalex-snapshot
Combined phylogeny and new classification of catsharks (Chondrichthyes: Elasmobranchii: Carcharhiniformes)
inferred← citeshttps://doi.org/10.1098/rspb.2011.2011openalex-snapshot
Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling
inferred← citeshttps://doi.org/10.1098/rstb.2005.1735openalex-snapshot
From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction
inferred← citeshttps://doi.org/10.1101/2020.11.09.375196openalex-snapshot
Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)
inferred← citeshttps://doi.org/10.1105/tpc.106.041111openalex-snapshot
Independent Ancient Polyploidy Events in the Sister Families Brassicaceae and Cleomaceae
inferred← citeshttps://doi.org/10.1109/bigdata.congress.2014.105openalex-snapshot
Enumerating Maximal Bicliques from a Large Graph Using MapReduce
inferred← citeshttps://doi.org/10.1109/tkde.2007.190660openalex-snapshot
Maximal Biclique Subgraphs and Closed Pattern Pairs of the Adjacency Matrix: A One-to-One Correspondence and Mining Algorithms
inferred← citeshttps://doi.org/10.1109/tmscs.2018.2802920openalex-snapshot
Incremental Maintenance of Maximal Bicliques in a Dynamic Bipartite Graph
inferred← citeshttps://doi.org/10.1109/tsc.2016.2523997openalex-snapshot
Enumerating Maximal Bicliques from a Large Graph Using MapReduce
inferred← citeshttps://doi.org/10.1111/2041-210x.13790openalex-snapshot
Rapid alignment updating with Extensiphy
inferred← citeshttps://doi.org/10.1111/cla.12127openalex-snapshot
A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homoplasy
inferred← citeshttps://doi.org/10.1111/cla.12150openalex-snapshot
Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree‐alignment and similarity‐alignment
inferred← citeshttps://doi.org/10.1111/cla.12196openalex-snapshot
The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes
inferred← citeshttps://doi.org/10.1111/cla.12447openalex-snapshot
Total evidence and sensitivity phylogenetic analyses of egg‐brooding frogs (Anura: Hemiphractidae)
inferred← citeshttps://doi.org/10.1111/j.0014-3820.2005.tb00953.xopenalex-snapshot
REPLICATE PATTERNS OF SPECIES RICHNESS, HISTORICAL BIOGEOGRAPHY, AND PHYLOGENY IN HOLARCTIC TREEFROGS
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2009.01342.xopenalex-snapshot
Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation
inferred← citeshttps://doi.org/10.1111/j.1096-0031.2009.00289.xopenalex-snapshot
The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries
inferred← citeshttps://doi.org/10.1111/j.1096-0031.2012.00411.xopenalex-snapshot
Phylogenetic placement of pelican spiders (Archaeidae, Araneae), with insight into evolution of the “neck” and predatory behaviours of the superfamily Palpimanoidea
inferred← citeshttps://doi.org/10.1111/j.1096-3642.2010.00644.xopenalex-snapshot
Beyond the prolegomenon: a molecular phylogeny of the Australian camaenid land snail radiation
inferred← citeshttps://doi.org/10.1111/j.1420-9101.2009.01717.xopenalex-snapshot
Why colour in subterranean vertebrates? Exploring the evolution of colour patterns in caecilian amphibians
inferred← citeshttps://doi.org/10.1111/j.1469-0691.2007.01786.xopenalex-snapshot
Guidelines for the validation and application of typing methods for use in bacterial epidemiology
inferred← citeshttps://doi.org/10.1111/j.1550-7408.2009.00464.xopenalex-snapshot
Two New Species of Trypanosomatid Parasites Isolated from Heteroptera in Costa Rica
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2007.00085.xopenalex-snapshot
A PHYLOGENETIC PERSPECTIVE ON ELEVATIONAL SPECIES RICHNESS PATTERNS IN MIDDLE AMERICAN TREEFROGS: WHY SO FEW SPECIES IN LOWLAND TROPICAL RAINFORESTS?
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2007.00159.xopenalex-snapshot
LOSS AND RE-EVOLUTION OF COMPLEX LIFE CYCLES IN MARSUPIAL FROGS: DOES ANCESTRAL TRAIT RECONSTRUCTION MISLEAD?
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2008.00519.xopenalex-snapshot
CONTINUOUS AND ARRESTED MORPHOLOGICAL DIVERSIFICATION IN SISTER CLADES OF CHARACIFORM FISHES: A PHYLOMORPHOSPACE APPROACH
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2009.00680.xopenalex-snapshot
CAN PARALLEL DIVERSIFICATION OCCUR IN SYMPATRY? REPEATED PATTERNS OF BODY-SIZE EVOLUTION IN COEXISTING CLADES OF NORTH AMERICAN SALAMANDERS
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2009.00790.xopenalex-snapshot
DID EGG-LAYING BOAS BREAK DOLLO'S LAW? PHYLOGENETIC EVIDENCE FOR REVERSAL TO OVIPARITY IN SAND BOAS (ERYX: BOIDAE)
inferred← citeshttps://doi.org/10.1111/j.1600-0587.2012.07773.xopenalex-snapshot
Building megaphylogenies for macroecology: taking up the challenge
inferred← citeshttps://doi.org/10.1111/nyas.12747openalex-snapshot
Estimating phylogenetic trees from genome‐scale data
inferred← citeshttps://doi.org/10.1111/syen.12490openalex-snapshot
The phylogeny of robber flies (Asilidae) inferred from ultraconserved elements
inferred← citeshttps://doi.org/10.1111/zsc.12007openalex-snapshot
Multilocus phylogeny reveals unexpected diversification patterns in A sian wolf snakes (genus L ycodon)
inferred← citeshttps://doi.org/10.1111/zsc.12210openalex-snapshot
Phylogenomic subsampling: a brief review
inferred← citeshttps://doi.org/10.1126/science.1102293openalex-snapshot
Ventilation of the Glacial Deep Pacific Ocean
inferred← citeshttps://doi.org/10.1126/science.1106198openalex-snapshot
Genomic Databases and the Tree of Life
inferred← citeshttps://doi.org/10.1126/science.1116759openalex-snapshot
Animal Evolution and the Molecular Signature of Radiations Compressed in Time
inferred← citeshttps://doi.org/10.1128/9781555815882.ch13openalex-snapshot
Phylogenetic and Genomic Analysis
inferred← citeshttps://doi.org/10.1137/1.9781611972788.7openalex-snapshot
Maximal Quasi-Bicliques with Balanced Noise Tolerance: Concepts and Co-clustering Applications
inferred← citeshttps://doi.org/10.1137/1.9781611976465.140openalex-snapshot
Nearly Optimal Average-Case Complexity of Counting Bicliques Under SETH
inferred← citeshttps://doi.org/10.1142/9781860948732_0043openalex-snapshot
MODELING SPECIES-GENES DATA FOR EFFICIENT PHYLOGENETIC INFERENCE
inferred← citeshttps://doi.org/10.1145/3484983openalex-snapshot
Scalable Phylogeny Reconstruction with Disaggregated Near-memory Processing
inferred← citeshttps://doi.org/10.1146/annurev.ecolsys.35.112202.130205openalex-snapshot
Phylogenomics
inferred← citeshttps://doi.org/10.1146/annurev.micro.59.030804.121233openalex-snapshot
GENOME TREES AND THE NATURE OF GENOME EVOLUTION
inferred← citeshttps://doi.org/10.11606/d.17.2011.tde-26092011-154314openalex-snapshot
Filogenia do Complexo Drosophila Buzzatii (Grupo Repleta): Inferências de Análises Multilocus Mitocondriais e Nucleares.
inferred← citeshttps://doi.org/10.1177/117693430700300014openalex-snapshot
Efficient Tree Searches with Available Algorithms
inferred← citeshttps://doi.org/10.1186/1471-2105-14-348openalex-snapshot
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees
inferred← citeshttps://doi.org/10.1186/1471-2105-9-166openalex-snapshot
Fast NJ-like algorithms to deal with incomplete distance matrices
inferred← citeshttps://doi.org/10.1186/1471-2148-10-155openalex-snapshot
Phylogenomics with incomplete taxon coverage: the limits to inference
inferred← citeshttps://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferred← citeshttps://doi.org/10.1186/1471-2148-11-281openalex-snapshot
Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): Another star phylogeny?
inferred← citeshttps://doi.org/10.1186/1471-2148-11-300openalex-snapshot
What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades
inferred← citeshttps://doi.org/10.1186/1471-2148-11-64openalex-snapshot
The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis
inferred← citeshttps://doi.org/10.1186/1471-2148-13-214openalex-snapshot
A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree
inferred← citeshttps://doi.org/10.1186/1471-2148-13-93openalex-snapshot
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
inferred← citeshttps://doi.org/10.1186/1471-2148-7-44openalex-snapshot
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
inferred← citeshttps://doi.org/10.1186/1471-2148-7-s1-s2openalex-snapshot
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
inferred← citeshttps://doi.org/10.1186/1471-2148-7-s1-s3openalex-snapshot
Inferring angiosperm phylogeny from EST data with widespread gene duplication
inferred← citeshttps://doi.org/10.1186/1471-2148-8-83openalex-snapshot
Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers
inferred← citeshttps://doi.org/10.1186/1471-2148-8-95openalex-snapshot
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
inferred← citeshttps://doi.org/10.1186/1471-2148-9-37openalex-snapshot
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
inferred← citeshttps://doi.org/10.1186/1471-2148-9-61openalex-snapshot
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms
inferred← citeshttps://doi.org/10.1186/1741-7007-8-19openalex-snapshot
Rapid progress on the vertebrate tree of life
inferred← citeshttps://doi.org/10.1186/1741-7007-9-55openalex-snapshot
The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences
inferred← citeshttps://doi.org/10.1186/1745-6150-2-36openalex-snapshot
Evolutionary history of bacteriophages with double-stranded DNA genomes
inferred← citeshttps://doi.org/10.1186/1748-7188-5-37openalex-snapshot
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
inferred← citeshttps://doi.org/10.1186/s12862-018-1162-9openalex-snapshot
The prevalence of terraced treescapes in analyses of phylogenetic data sets
inferred← citeshttps://doi.org/10.1186/s12864-018-4619-8openalex-snapshot
The performance of coalescent-based species tree estimation methods under models of missing data
inferred← citeshttps://doi.org/10.1186/s13015-014-0022-4openalex-snapshot
A priori assessment of data quality in molecular phylogenetics
inferred← citeshttps://doi.org/10.1186/s43008-019-0018-2openalex-snapshot
Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)
inferred← citeshttps://doi.org/10.12705/632.33openalex-snapshot
Phylogeny of Cissus (Vitaceae) focusing on South American species
inferred← citeshttps://doi.org/10.1371/journal.pone.0010525openalex-snapshot
Assessing the Value of DNA Barcodes and Other Priority Gene Regions for Molecular Phylogenetics of Lepidoptera
inferred← citeshttps://doi.org/10.1371/journal.pone.0024851openalex-snapshot
Towards Resolving the Complete Fern Tree of Life
inferred← citeshttps://doi.org/10.1371/journal.pone.0025355openalex-snapshot
Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)
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