Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction.

By William J. Bruno, Nicholas D. Socci, A. Halpern. Molecular biology and evolution, 2000

523 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/f7e5619b041fa256f8175dab3ad14e150d3d2a2a

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Citations in the corpus

Molecular phylogenetics: principles and practice (2012, methodology): “Distance methods are also sensitive to gaps in the sequence alignment 38 .”
EARLY EVOLUTIONARY HISTORY OF DINOFLAGELLATES AND APICOMPLEXANS (ALVEOLATA) AS INFERRED FROM HSP90 AND ACTIN PHYLOGENIES 1 (2004, methodology): “Bootstrap distance trees were constructed with WEIGHBOR.”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, methodology): “The final alignment was used to reconstruct phylogenies with a series of phylogeny reconstruction methods: PHYML [150], Tree-Puzzle [151], Weighbor [152], and the protpars program from the PHYLIP package (version 3.6a3) [145].”
Congruent evidence from α-tubulin and β-tubulin gene phylogenies for a zygomycete origin of microsporidia (2003, methodology): “Trees were inferred by weighted neighbor-joining [using WEIGHBOR version 1.0.1 a (Bruno et al., 2000)] and Fitch–Margoliash [using FITCH version 3.6 a (Felsenstein, 1993)].”
Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle (2002, background): “The balanced NNI algorithm BNNI achieves a good level of performance, superior to that of NJ, BIONJ and WEIGHBOR.”
INVESTIGATIONS INTO SOUTHERN AUSTRALIAN ULVA (ULVOPHYCEAE, CHLOROPHYTA) TAXONOMY AND MOLECULAR PHYLOGENY INDICATE BOTH COSMOPOLITANISM AND ENDEMIC CRYPTIC SPECIES 1 (2010, methodology): “Trees were inferred using a weighted neighbor-joining (NJ) method from the program WEIGHBOR 1.0.1a (Bruno et al. 2000).”
Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold (2007, methodology): “Maximum-likelihood distance matrices were constructed using the TreePuzzle 5 program [130] and were used as input for the construction of neighbor-joining with the Weighbor program [131].”
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy (2007, methodology): “0 of Bergey’s taxonomic outline, along with additional sequences for four Alicyclobacillaceae species type strains that became available after the release of the outline (marked with an asterisk), and two Bacillus species type strains were analyzed using the weighted neighbor-joining method (5).”
Molecular data and the evolutionary history of dinoflagellates (2004, methodology): “3), and while the A. carterae group still holds together with good support and a relatively long branch, it is not at the base of the Gonyaulacales (in Weighbor and Fitch trees it interrupts a badly supported clade of Peridiniales).”
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006, methodology): “Selections containing both myRDP and public RDP sequences are used to create a phylogenetic tree using the Weighbor weighted neighbor-joining tree building algorithm (12).”
Ribosomal Database Project: data and tools for high throughput rRNA analysis (2013, methodology): “This tool uses the Weighbor (28) weighted neighbor joining method with Jukes–Cantor corrected distances calculated from the RDP alignment.”
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, background): “NJ and its variants (e.g., BIONJ that takes the variance of distance estimation into consideration) (Gascuel 1997; Bruno et al. 2000) were among the few available options for analyzing large data sets until the 2000s, and are still widely used today to quickly produce good starting points for more…”
The RDP-II (Ribosomal Database Project) (2001, methodology): “A new backbone phylogenetic tree for 217 prokaryotic SSU rRNA sequences was calculated using the WEIGHBOR algorithm (5).”
Genome Majority Vote Improves Gene Predictions (2011, methodology): “html) based on the known three-dimensional structure, and tree building with a maximum likelihood method employing a minimal model of protein functional pressure (RIND [25] and WEIGHBOR [26]).”
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy (2003, methodology): “Most of these trees are new since our last update and were created using the WEIGHBOR algorithm (2).”