247 related articles for article (PubMed ID: 36083447)
1. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.
Zhu Q; Mirarab S
Methods Mol Biol; 2022; 2569():137-165. PubMed ID: 36083447
[TBL] [Abstract][Full Text] [Related]
2. The net of life: reconstructing the microbial phylogenetic network.
Kunin V; Goldovsky L; Darzentas N; Ouzounis CA
Genome Res; 2005 Jul; 15(7):954-9. PubMed ID: 15965028
[TBL] [Abstract][Full Text] [Related]
3. Phylogenomic networks.
Dagan T
Trends Microbiol; 2011 Oct; 19(10):483-91. PubMed ID: 21820313
[TBL] [Abstract][Full Text] [Related]
4. Lateral gene transfer as a support for the tree of life.
Abby SS; Tannier E; Gouy M; Daubin V
Proc Natl Acad Sci U S A; 2012 Mar; 109(13):4962-7. PubMed ID: 22416123
[TBL] [Abstract][Full Text] [Related]
5. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.
Mendler K; Chen H; Parks DH; Lobb B; Hug LA; Doxey AC
Nucleic Acids Res; 2019 May; 47(9):4442-4448. PubMed ID: 31081040
[TBL] [Abstract][Full Text] [Related]
6. A Guide to Phylogenomic Inference.
Patané JSL; Martins J; Setubal JC
Methods Mol Biol; 2024; 2802():267-345. PubMed ID: 38819564
[TBL] [Abstract][Full Text] [Related]
7. A model of horizontal gene transfer and the bacterial phylogeny problem.
Galtier N
Syst Biol; 2007 Aug; 56(4):633-42. PubMed ID: 17661231
[TBL] [Abstract][Full Text] [Related]
8. Incongruence in the phylogenomics era.
Steenwyk JL; Li Y; Zhou X; Shen XX; Rokas A
Nat Rev Genet; 2023 Dec; 24(12):834-850. PubMed ID: 37369847
[TBL] [Abstract][Full Text] [Related]
9. Genome trees constructed using five different approaches suggest new major bacterial clades.
Wolf YI; Rogozin IB; Grishin NV; Tatusov RL; Koonin EV
BMC Evol Biol; 2001 Oct; 1():8. PubMed ID: 11734060
[TBL] [Abstract][Full Text] [Related]
10. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.
Zhu Q; Mai U; Pfeiffer W; Janssen S; Asnicar F; Sanders JG; Belda-Ferre P; Al-Ghalith GA; Kopylova E; McDonald D; Kosciolek T; Yin JB; Huang S; Salam N; Jiao JY; Wu Z; Xu ZZ; Cantrell K; Yang Y; Sayyari E; Rabiee M; Morton JT; Podell S; Knights D; Li WJ; Huttenhower C; Segata N; Smarr L; Mirarab S; Knight R
Nat Commun; 2019 Dec; 10(1):5477. PubMed ID: 31792218
[TBL] [Abstract][Full Text] [Related]
11. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.
Bernard G; Stephens TG; González-Pech RA; Chan CX
Methods Mol Biol; 2021; 2242():69-76. PubMed ID: 33961218
[TBL] [Abstract][Full Text] [Related]
12. A simple method for phylogenomic inference using the information of gene content of genomes.
Zhang H; Zhong Y; Hao B; Gu X
Gene; 2009 Jul; 441(1-2):163-8. PubMed ID: 18675889
[TBL] [Abstract][Full Text] [Related]
13. Concatenated alignments and the case of the disappearing tree.
Thiergart T; Landan G; Martin WF
BMC Evol Biol; 2014 Dec; 14():266. PubMed ID: 25547755
[TBL] [Abstract][Full Text] [Related]
14. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.
Bromberg R; Grishin NV; Otwinowski Z
PLoS Comput Biol; 2016 Jun; 12(6):e1004985. PubMed ID: 27336403
[TBL] [Abstract][Full Text] [Related]
15. An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.
Rangel LT; Soucy SM; Setubal JC; Gogarten JP; Fournier GP
Genome Biol Evol; 2021 Sep; 13(9):. PubMed ID: 34390574
[TBL] [Abstract][Full Text] [Related]
16. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction.
Na SI; Kim YO; Yoon SH; Ha SM; Baek I; Chun J
J Microbiol; 2018 Apr; 56(4):280-285. PubMed ID: 29492869
[TBL] [Abstract][Full Text] [Related]
17. The impact of automated filtering of BLAST-determined homologs in the phylogenetic detection of horizontal gene transfer from a transcriptome assembly.
Wisecaver JH; Hackett JD
Mol Phylogenet Evol; 2014 Feb; 71():184-92. PubMed ID: 24321593
[TBL] [Abstract][Full Text] [Related]
18. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups.
Wu D; Jospin G; Eisen JA
PLoS One; 2013; 8(10):e77033. PubMed ID: 24146954
[TBL] [Abstract][Full Text] [Related]
19. Genome phylogeny based on gene content.
Snel B; Bork P; Huynen MA
Nat Genet; 1999 Jan; 21(1):108-10. PubMed ID: 9916801
[TBL] [Abstract][Full Text] [Related]
20. Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids.
Grant JR; Katz LA
Genome Biol Evol; 2014 Sep; 6(9):2350-60. PubMed ID: 25146649
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]