Literature DB >> 33234569

Feature frequency profile-based phylogenies are inaccurate.

Yuanning Li1, Kyle T David2, Xing-Xing Shen3, Jacob L Steenwyk1, Kenneth M Halanych2, Antonis Rokas4.   

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Year:  2020        PMID： 33234569      PMCID： PMC7749326          DOI： 10.1073/pnas.2013143117

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  7 in total

1.  Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions.

Authors:  Gregory E Sims; Se-Ran Jun; Guohong A Wu; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-02       Impact factor: 11.205

2.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

Authors:  O Gascuel
Journal:  Mol Biol Evol       Date:  1997-07       Impact factor: 16.240

3.  A genome Tree of Life for the Fungi kingdom.

Authors:  JaeJin Choi; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-14       Impact factor: 11.205

4.  A new view of the tree of life.

Authors:  Laura A Hug; Brett J Baker; Karthik Anantharaman; Christopher T Brown; Alexander J Probst; Cindy J Castelle; Cristina N Butterfield; Alex W Hernsdorf; Yuki Amano; Kotaro Ise; Yohey Suzuki; Natasha Dudek; David A Relman; Kari M Finstad; Ronald Amundson; Brian C Thomas; Jillian F Banfield
Journal:  Nat Microbiol       Date:  2016-04-11       Impact factor: 17.745

5.  Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.

Authors:  Xing-Xing Shen; Dana A Opulente; Jacek Kominek; Xiaofan Zhou; Jacob L Steenwyk; Kelly V Buh; Max A B Haase; Jennifer H Wisecaver; Mingshuang Wang; Drew T Doering; James T Boudouris; Rachel M Schneider; Quinn K Langdon; Moriya Ohkuma; Rikiya Endoh; Masako Takashima; Ri-Ichiroh Manabe; Neža Čadež; Diego Libkind; Carlos A Rosa; Jeremy DeVirgilio; Amanda Beth Hulfachor; Marizeth Groenewald; Cletus P Kurtzman; Chris Todd Hittinger; Antonis Rokas
Journal:  Cell       Date:  2018-11-08       Impact factor: 41.582

Review 6.  Application and accuracy of molecular phylogenies.

Authors:  D M Hillis; J P Huelsenbeck; C W Cunningham
Journal:  Science       Date:  1994-04-29       Impact factor: 47.728

7.  Whole-proteome tree of life suggests a deep burst of organism diversity.

Authors:  JaeJin Choi; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2020-02-04       Impact factor: 11.205
  7 in total
  3 in total

1.  Reply to Li et al.: Organism tree of life: Gene phylogeny vs. whole-proteome phylogeny.

Authors:  JaeJin Choi; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-24       Impact factor: 11.205

2.  A genome-scale phylogeny of the kingdom Fungi.

Authors:  Yuanning Li; Jacob L Steenwyk; Ying Chang; Yan Wang; Timothy Y James; Jason E Stajich; Joseph W Spatafora; Marizeth Groenewald; Casey W Dunn; Chris Todd Hittinger; Xing-Xing Shen; Antonis Rokas
Journal:  Curr Biol       Date:  2021-02-18       Impact factor: 10.834

3.  Phylogenies from unaligned proteomes using sequence environments of amino acid residues.

Authors:  Juan Carlos Aledo
Journal:  Sci Rep       Date:  2022-05-06       Impact factor: 4.996
  3 in total

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