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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
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.tree.2009.01.009openalex-snapshot
Gene tree discordance, phylogenetic inference and the multispecies coalescent
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.013openalex-snapshot
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1086/317584openalex-snapshot
Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes
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/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/sys070openalex-snapshot
The Evolutionary Root of Flowering Plants
inferredcites →https://doi.org/10.1093/sysbio/syt108openalex-snapshot
Another Look at the Root of the Angiosperms Reveals a Familiar Tale
inferredcites →https://doi.org/10.1093/sysbio/syu055openalex-snapshot
Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
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/10.1111/j.1469-8137.2012.04212.xopenalex-snapshot
Highly conserved low‐copy nuclear genes as effective markers for phylogenetic analyses in angiosperms
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s11openalex-snapshot
BBCA: Improving the scalability of *BEAST using random binning
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s7openalex-snapshot
Disk covering methods improve phylogenomic analyses
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0027731openalex-snapshot
RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation
inferredcites →https://doi.org/10.4172/2329-9002.1000110openalex-snapshot
Error in Phylogenetic Estimation for Bushes in the Tree of Life
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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inferred← citeshttps://doi.org/10.1002/ajb2.1052openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/aps3.11400openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.cub.2020.09.051openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.dib.2019.104271openalex-snapshot
Genome assembly and phylogenomic data analyses using plastid data: Contrasting species tree estimation methods
inferred← citeshttps://doi.org/10.1016/j.fgb.2023.103862openalex-snapshot
Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes
inferred← citeshttps://doi.org/10.1016/j.gloplacha.2022.103757openalex-snapshot
Volcanic events coincide with plant dispersal across the Northern Andes
inferred← citeshttps://doi.org/10.1016/j.heliyon.2020.e05583openalex-snapshot
Markers for genetic change
inferred← citeshttps://doi.org/10.1016/j.hpj.2022.06.005openalex-snapshot
Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2021.06.186openalex-snapshot
Hb adaptation to hypoxia in high-altitude fishes: Fresh evidence from schizothoracinae fishes in the Qinghai-Tibetan Plateau
inferred← citeshttps://doi.org/10.1016/j.ijpara.2022.03.005openalex-snapshot
Phylogenomics and host-switching patterns of Philopteridae (Psocodea: Phthiraptera) feather lice
inferred← citeshttps://doi.org/10.1016/j.isci.2020.101124openalex-snapshot
Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization
inferred← citeshttps://doi.org/10.1016/j.isci.2023.107684openalex-snapshot
Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae
inferred← citeshttps://doi.org/10.1016/j.jtbi.2016.11.005openalex-snapshot
Species tree estimation using Neighbor Joining
inferred← citeshttps://doi.org/10.1016/j.jtbi.2022.111078openalex-snapshot
Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: Theory and applications
inferred← citeshttps://doi.org/10.1016/j.margen.2019.02.003openalex-snapshot
Diatom genes originating from red and green algae: Implications for the secondary endosymbiosis models
inferred← citeshttps://doi.org/10.1016/j.margen.2021.100863openalex-snapshot
Description of four Millepora spp. transcriptomes and their potential to delimit the Caribbean fire coral species
inferred← citeshttps://doi.org/10.1016/j.pld.2025.07.003openalex-snapshot
Genome analyses provide insights into Engelhardia’s adaptation to East Asia summer monsoon
inferred← citeshttps://doi.org/10.1016/j.sajb.2025.05.058openalex-snapshot
Biome shifts and recent rapid radiations in the Cape Clade of the genus Indigofera (Fabaceae: Indigofereae) explain contemporary diversity in the GCFR
inferred← citeshttps://doi.org/10.1016/j.sajb.2025.08.006openalex-snapshot
Refined generic and infrageneric classification of the Cape Psoraleeae clade (Fabaceae) – taxonomic studies in the phylogenomic era
inferred← citeshttps://doi.org/10.1016/j.tig.2020.08.012openalex-snapshot
New Approaches for Inferring Phylogenies in the Presence of Paralogs
inferred← citeshttps://doi.org/10.1016/j.ygeno.2022.110394openalex-snapshot
High-quality chromosome-level genome assembly of Litsea coreana L. provides insights into Magnoliids evolution and flavonoid biosynthesis
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.10.027openalex-snapshot
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.12.013openalex-snapshot
The effects of subsampling gene trees on coalescent methods applied to ancient divergences
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.02.003openalex-snapshot
Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.030openalex-snapshot
Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.06.007openalex-snapshot
Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.07.002openalex-snapshot
Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.08.011openalex-snapshot
Evolutionary history of chloridoid grasses estimated from 122 nuclear loci
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.12.006openalex-snapshot
Restructuring higher taxonomy using broad-scale phylogenomics: The living Ophiuroidea
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.01.006openalex-snapshot
Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.03.002openalex-snapshot
Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.03.014openalex-snapshot
Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.03.017openalex-snapshot
Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.03.022openalex-snapshot
The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.04.001openalex-snapshot
Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.04.003openalex-snapshot
Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.04.016openalex-snapshot
Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-sequencing
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.05.002openalex-snapshot
Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.05.004openalex-snapshot
Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.06.013openalex-snapshot
Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.07.009openalex-snapshot
Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.07.018openalex-snapshot
Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.08.009openalex-snapshot
The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.09.013openalex-snapshot
Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.09.021openalex-snapshot
Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.10.001openalex-snapshot
Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.10.008openalex-snapshot
Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.10.013openalex-snapshot
Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.11.005openalex-snapshot
Using a new RAD-sequencing approach to study the evolution of Micromeria in the Canary islands
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.11.008openalex-snapshot
Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.12.026openalex-snapshot
Molecular systematics and phylogenetic analysis of the Asian endemic freshwater sleepers (Gobiiformes: Odontobutidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.12.029openalex-snapshot
Light in the darkness: New perspective on lanternfish relationships and classification using genomic and morphological data
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.02.016openalex-snapshot
Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.02.017openalex-snapshot
Hidden diversity of forest birds in Madagascar revealed using integrative taxonomy
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.02.021openalex-snapshot
Complex taxonomy of the ‘brush tail’ peregrine earthworm Pontoscolex corethrurus
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.03.006openalex-snapshot
SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.03.014openalex-snapshot
Revised classification of the righteye flounders (Teleostei: Pleuronectidae) based on multilocus phylogeny with complete taxon sampling
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.04.008openalex-snapshot
Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.05.005openalex-snapshot
Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.06.002openalex-snapshot
Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.07.014openalex-snapshot
Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.07.018openalex-snapshot
Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.08.007openalex-snapshot
Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.001openalex-snapshot
Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.003openalex-snapshot
Phylogenomics, life history and morphological evolution of ophiocomid brittlestars
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.012openalex-snapshot
Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.021openalex-snapshot
Multiple connections between Amazonia and Atlantic Forest shaped the phylogenetic and morphological diversity of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.033openalex-snapshot
Multi-allele species reconstruction using ASTRAL
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.037openalex-snapshot
Molecular phylogeny of Caudofoveata (Mollusca) challenges traditional views
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.039openalex-snapshot
Four hundred shades of brown: Higher level phylogeny of the problematic Euptychiina (Lepidoptera, Nymphalidae, Satyrinae) based on hybrid enrichment data
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.01.003openalex-snapshot
Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.02.017openalex-snapshot
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.02.021openalex-snapshot
Phylogenomics facilitates stable scorpion systematics: Reassessing the relationships of Vaejovidae and a new higher-level classification of Scorpiones (Arachnida)
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.02.022openalex-snapshot
Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.03.007openalex-snapshot
Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.03.017openalex-snapshot
Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.05.002openalex-snapshot
Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.05.022openalex-snapshot
Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.05.023openalex-snapshot
Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106534openalex-snapshot
NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias)
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106535openalex-snapshot
Phylogeography of the Rufous Vanga and the role of bioclimatic transition zones in promoting speciation within Madagascar
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106539openalex-snapshot
Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106589openalex-snapshot
Relicts and radiations: Phylogenomics of an Australasian lizard clade with east Gondwanan origins (Gekkota: Diplodactyloidea)
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106605openalex-snapshot
Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements
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