Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle

By Richard Desper, Olivier Gascuel. Workshop on Algorithms in Bioinformatics, 2002

515 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/6f67aac0d20c3a42e0e3f83595d9a54cd60d9ce7

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Citations in the corpus

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program (2015, methodology): “We proposed fast, BME-based algorithms (Desper and Gascuel 2002, 2004) to 1) construct an initial tree using greedy taxon insertion and 2) perform topological moves, namely Nearest Neighbor Interchanges (NNIs), to improve an initial (e.g., NJ) tree.”
Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions (2022, methodology): “As shown in Figure 4(e), the trajectory inference with the RNA-FM embedding of the virus genome is roughly in line with the phylogenetic tree generated by FastME [56], which is considered the ground truth (Figure 4(d)).”
Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster (2012, methodology): “The distance matrix was analyzed using the FastME minimum evolution model (Desper & Gascuel 2002) running on the South of France Bioinformatics Platform web server (http://www.atgc-montpellier.fr/fastme/).”
COBALT: constraint-based alignment tool for multiple protein sequences (2007, result): “The guide tree can optionally be constructed using fast minimum evolution (FASTme) (Desper and Gascuel, 2002), but we did not do so in the results presented here.”
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix (2009, methodology): “FastME is another minimum evolution method that takes only O( N 2 ) time (Desper and Gascuel 2002).”
ViPR: an open bioinformatics database and analysis resource for virology research (2011, methodology): “The data in ViPR can be analyzed using a suite of comparative genomics analysis and visualization tools including phylogenetic tree reconstruction with the FastME, RAxML or PhyML algorithms (18) (19) (20) , tree manipulation with Archaeopteryx (21) and evolutionary model optimization with modelTest ”
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy (2012, methodology): “They were built using pair-wise distance computations (not taking introns as differences as explained above) and FastMe (14).”
DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution (2013, methodology): “First, in addition to the popular neighbor-joining (NJ) method (Saitou and Nei 1987), DAMBE implements the fast and accurate FastME method (Desper and Gascuel 2002), which not only has a global criterion for the best tree, in contrast to a local criterion in the NJ method, but also extensive…”
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments (2010, methodology): “) Conversely, on nucleotide simulations with 24 sequences that (unrealistically) do not contain any rate variation across sites (the fast-evolving alignments of [12]), the CAT model only reduces accuracy slightly, from 93.”