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Are theoretical advances in distance-based tree learning practical for phylogenetic inference?

https://doi.org/10.64898/2026.01.12.698017
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Outgoing claims: the papers this work cites, builds on, or argues with.

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A few logs suffice to build (almost) all trees (I)
inferredcites →https://doi.org/10.1002/rsa.20372openalex-snapshot
Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges
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Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
inferredcites →https://doi.org/10.1007/978-3-642-69024-2_34openalex-snapshot
Theoretical and Computational Considerations of the Compatibility of Qualitative Taxonomic Characters
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/bfb0045079openalex-snapshot
Parsimony is hard to beat!
inferredcites →https://doi.org/10.1007/pl00008277openalex-snapshot
The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction
inferredcites →https://doi.org/10.1007/s002390010118openalex-snapshot
Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies
inferredcites →https://doi.org/10.1007/s00440-009-0246-2openalex-snapshot
Evolutionary trees and the Ising model on the Bethe lattice: a proof of Steel’s conjecture
inferredcites →https://doi.org/10.1007/s00453-007-9116-4openalex-snapshot
Why Neighbor-Joining Works
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.mbs.2003.10.004openalex-snapshot
A phase transition for a random cluster model on phylogenetic trees
inferredcites →https://doi.org/10.1016/j.mbs.2005.11.003openalex-snapshot
A signal-to-noise analysis of phylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences
inferredcites →https://doi.org/10.1016/j.tim.2017.09.004openalex-snapshot
Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology
inferredcites →https://doi.org/10.1016/s0196-6774(03)00049-xopenalex-snapshot
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
inferredcites →https://doi.org/10.1016/s0304-3975(99)00028-6openalex-snapshot
A few logs suffice to build (almost) all trees: Part II
inferredcites →https://doi.org/10.1016/s1360-1385(03)00165-1openalex-snapshot
The challenge of constructing large phylogenetic trees
inferredcites →https://doi.org/10.1089/10665270252935467openalex-snapshot
Fast Recovery of Evolutionary Trees with Thousands of Nodes
inferredcites →https://doi.org/10.1089/106652703322539015openalex-snapshot
On the Impossibility of Reconstructing Ancestral Data and Phylogenies
inferredcites →https://doi.org/10.1089/106652799318337openalex-snapshot
Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
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/bty633openalex-snapshot
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
inferredcites →https://doi.org/10.1093/bioinformatics/btz344openalex-snapshot
TreeMerge: a new method for improving the scalability of species tree estimation methods
inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
inferredcites →https://doi.org/10.1093/molbev/msac092openalex-snapshot
AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era
inferredcites →https://doi.org/10.1093/molbev/msj059openalex-snapshot
Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026231openalex-snapshot
Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/43.3.329openalex-snapshot
Statistical Properties of the Maximum Likelihood Method of Phylogenetic Estimation and Comparison With Distance Matrix Methods
inferredcites →https://doi.org/10.1093/ve/vey016openalex-snapshot
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
inferredcites →https://doi.org/10.1109/tcbb.2007.1010openalex-snapshot
Distorted Metrics on Trees and Phylogenetic Forests
inferredcites →https://doi.org/10.1111/j.1558-5646.1984.tb00255.xopenalex-snapshot
DISTANCE METHODS FOR INFERRING PHYLOGENIES: A JUSTIFICATION
inferredcites →https://doi.org/10.1137/s0097539798342496openalex-snapshot
Evolutionary Trees Can be Learned in Polynomial Time in the Two-State General Markov Model
inferredcites →https://doi.org/10.1145/1060590.1060645openalex-snapshot
Learning nonsingular phylogenies and hidden Markov models
inferredcites →https://doi.org/10.1145/1132516.1132540openalex-snapshot
Optimal phylogenetic reconstruction
inferredcites →https://doi.org/10.1146/annurev-ecolsys-102209-144710openalex-snapshot
Phylogenetic Methods in Biogeography
inferredcites →https://doi.org/10.1146/annurev.ecolsys.28.1.437openalex-snapshot
Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood
inferredcites →https://doi.org/10.1186/s12864-020-6605-1openalex-snapshot
Unblended disjoint tree merging using GTM improves species tree estimation
inferredcites →https://doi.org/10.1371/journal.pcbi.1002947openalex-snapshot
Viral Phylodynamics
inferredcites →https://doi.org/10.2307/1447682openalex-snapshot
Molecular Systematics
inferredcites →https://doi.org/10.2307/2412810openalex-snapshot
The Number of Evolutionary Trees
inferredcites →https://doi.org/10.3390/a14050148openalex-snapshot
Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation
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