FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Citations
10,010 citations
Cites methods or result from "FastTree: Computing Large Minimum E..."
...The simulated protein alignments and the genuine COG alignments were described previously [2]....
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...0 is more accurate than most other minimum-evolution methods, but not as accurate as maximum-likelihood methods [2]....
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...We tested FastTree on simulated protein alignments with 250 to 5,000 sequences [2]....
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...Nevertheless, FastTree with NNIs and FastME with NNIs give very similar results [2], and computing the exact change in total tree length does not improve the accuracy of FastTree’s SPRs (data not shown)....
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...For example, on simulated protein alignments with just 10 sequences (from [2]), adding the CAT model improves FastTree’s accuracy from 76....
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6,767 citations
Cites methods from "FastTree: Computing Large Minimum E..."
...reference collection using fasttree (23) was used for the calculation of phylogeny-based α and β diversity metrics....
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5,788 citations
Cites background from "FastTree: Computing Large Minimum E..."
...1.3 (Price et al. 2009) under the WAG (Whelan and Goldman Genome Research 1051 www.genome.org 2001) andGAMMA (Yang 1994)models....
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3,640 citations
Cites methods from "FastTree: Computing Large Minimum E..."
...Taxonomy was assigned using the Ribosomal Database Project (RDP) classifier with a minimum support threshold of 60% (42) and the RDP taxonomic nomenclature....
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2,966 citations
Cites methods from "FastTree: Computing Large Minimum E..."
...Phylogenetic trees were then built from all representative sequences using the FastTree algorithm (Price et al., 2009)....
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References
57,055 citations
"FastTree: Computing Large Minimum E..." refers methods in this paper
...Given an alignment, Neighbor-Joining and related minimum evolution methods are the fastest and most scalable approaches for inferring phylogenies (Saitou and Nei, 1987; Studier and Keppler, 1988; Desper and Gascuel, 2002)....
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...FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix...
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40,349 citations
"FastTree: Computing Large Minimum E..." refers methods in this paper
...…is to use the bootstrap: to resample the columns of the alignment, to rerun the method 100– 1,000 times, to compare the resulting trees to each other or to the tree inferred from the full alignment, and to count the number of times that each split occurs in the resulting trees (Felsenstein 1985)....
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...FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix...
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37,524 citations
"FastTree: Computing Large Minimum E..." refers background in this paper
...A faster UPGMA variant of FastTree is available at http://www.microbesonline.org/fasttree and might be useful for this purpose, both because of its speed and because UPGMA guide trees may lead to better alignments ( Edgar, 2004 )....
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16,496 citations
"FastTree: Computing Large Minimum E..." refers methods in this paper
...To quantify how effective the measures were in distinguishing correct splits, we used the area under the receiver operating characteristic curve (AOC, DeLong and Clarke-Pearson (1998))....
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16,261 citations
"FastTree: Computing Large Minimum E..." refers methods in this paper
...To quantify the quality of each topology, we used PhyML to optimize the branch lengths and compute the log likelihood....
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...To quantify the quality of each topology, we used PhyML with the Hasegawa–Kishino–Yano 85 model, which accounts for the higher rate of transitions over transversions, and four categories of gamma-distributed rates....
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...(Despite the high usage of virtual memory by PhyML, both PhyML and RAxML ran at over 99% CPU utilization.)...
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...We ran PhyML with the Jones, Taylor, and Thorton (JTT) model of amino acid substitution and four categories of gamma-distributed rates....
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...Even for COG alignments of just 1,250 proteins, PhyML 3 typically took over a week....
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