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COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory

https://doi.org/10.1101/2020.11.17.387399
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00285-009-0260-0openalex-snapshot
Maximum tree: a consistent estimator of the species tree
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Evolution of Protein Molecules
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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
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Estimating diversification rates from phylogenetic information
inferredcites →https://doi.org/10.1016/j.ympev.2012.07.004openalex-snapshot
Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy
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/10.1016/j.ympev.2014.10.004openalex-snapshot
When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
inferredcites →https://doi.org/10.1016/j.ympev.2017.03.017openalex-snapshot
Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes
inferredcites →https://doi.org/10.1038/nature13679openalex-snapshot
Gibbon genome and the fast karyotype evolution of small apes
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/18.2.337openalex-snapshot
Generating samples under a Wright–Fisher neutral model of genetic variation
inferredcites →https://doi.org/10.1093/bioinformatics/btn484openalex-snapshot
BEST: Bayesian estimation of species trees under the coalescent model
inferredcites →https://doi.org/10.1093/bioinformatics/btp079openalex-snapshot
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
inferredcites →https://doi.org/10.1093/bioinformatics/btq539openalex-snapshot
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
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/czoolo/61.5.854openalex-snapshot
The BPP program for species tree estimation and species delimitation
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/msx277openalex-snapshot
Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons
inferredcites →https://doi.org/10.1093/molbev/msy147openalex-snapshot
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/molbev/msz296openalex-snapshot
A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syp047openalex-snapshot
What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
inferredcites →https://doi.org/10.1093/sysbio/syq047openalex-snapshot
Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods
inferredcites →https://doi.org/10.1093/sysbio/syq073openalex-snapshot
The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
inferredcites →https://doi.org/10.1093/sysbio/syt061openalex-snapshot
Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales
inferredcites →https://doi.org/10.1093/sysbio/syw021openalex-snapshot
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
inferredcites →https://doi.org/10.1111/ele.12144openalex-snapshot
Rates of projected climate change dramatically exceed past rates of climatic niche evolution among vertebrate species
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/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1371/currents.tol.34260cc27551a527b124ec5f6334b6beopenalex-snapshot
Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated conditions
inferredcites →https://doi.org/10.1371/journal.pone.0054848openalex-snapshot
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0129183openalex-snapshot
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
inferredcites →https://doi.org/10.1534/genetics.115.174425openalex-snapshot
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2025.10.20.683470openalex-snapshot
Composite Likelihood Adjustment in Bayesian Inference for Estimating Species Tree Parameters Under the Multispecies Coalescent
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