Pandi-Perumal S, Saravanan K, Paul S, Spence D, Chidambaram S
Int J Mol Sci. 2025; 26(1.
PMID: 39795919
PMC: 11719702.
DOI: 10.3390/ijms26010060.
Bonnici V, Chicco D
BioData Min. 2024; 17(1):28.
PMID: 39227987
PMC: 11370085.
DOI: 10.1186/s13040-024-00380-2.
Furni F, Secchi E, Speller C, DenDanto D, Ramp C, Larsen F
Syst Biol. 2024; 73(6):873-885.
PMID: 39158356
PMC: 11637684.
DOI: 10.1093/sysbio/syae049.
Riesco R, Trujillo M
Int J Syst Evol Microbiol. 2024; 74(3).
PMID: 38512750
PMC: 10963913.
DOI: 10.1099/ijsem.0.006300.
Na S, Bailey M, Chalita M, Cho J, Chun J
J Microbiol. 2023; 61(7):683-692.
PMID: 37566173
DOI: 10.1007/s12275-023-00064-2.
Phylogenomic Testing of Root Hypotheses.
Tria F, Landan G, Picazo D, Dagan T
Genome Biol Evol. 2023; 15(6).
PMID: 37247390
PMC: 10262964.
DOI: 10.1093/gbe/evad096.
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi.
Kim D, Gilchrist C, Chun J, Steinegger M
Nucleic Acids Res. 2022; 51(D1):D777-D784.
PMID: 36271795
PMC: 9825530.
DOI: 10.1093/nar/gkac894.
Annotation-free delineation of prokaryotic homology groups.
Yin Y, Ogilvie H, Nakhleh L
PLoS Comput Biol. 2022; 18(6):e1010216.
PMID: 35675326
PMC: 9212150.
DOI: 10.1371/journal.pcbi.1010216.
Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.
Schull J, Turakhia Y, Hemker J, Dally W, Bejerano G
Genome Biol Evol. 2022; 14(3).
PMID: 35171243
PMC: 8920512.
DOI: 10.1093/gbe/evac013.
Comparative Genome Analysis of Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes.
Liu H, Prajapati V, Prajapati S, Bais H, Lu J
Front Genet. 2021; 12:724217.
PMID: 34659348
PMC: 8514880.
DOI: 10.3389/fgene.2021.724217.
AniProtDB: A Collection of Consistently Generated Metazoan Proteomes for Comparative Genomics Studies.
Barreira S, Nguyen A, Fredriksen M, Wolfsberg T, Moreland R, Baxevanis A
Mol Biol Evol. 2021; 38(10):4628-4633.
PMID: 34048573
PMC: 8476134.
DOI: 10.1093/molbev/msab165.
Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology.
Chakraborty C, Sharma A, Sharma G, Bhattacharya M, Patra B, Sarkar B
Genes Genomics. 2021; 43(7):759-773.
PMID: 33884571
DOI: 10.1007/s13258-021-01089-w.
Taxogenomic and Comparative Genomic Analysis of the Genus Focused on the Identification of Biosynthetic Clusters PKS and NRPS.
Ramirez-Duran N, de la Haba R, Vera-Gargallo B, Sanchez-Porro C, Alonso-Carmona S, Sandoval-Trujillo H
Front Microbiol. 2021; 12:603791.
PMID: 33776952
PMC: 7990883.
DOI: 10.3389/fmicb.2021.603791.
Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes.
Maruyama S, Aparecida Rogerio L, Freitas P, Teixeira M, Ribeiro J
Sci Rep. 2021; 11(1):3791.
PMID: 33589693
PMC: 7884790.
DOI: 10.1038/s41598-021-81926-w.
A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes.
Avni E, Snir S
Sci Rep. 2020; 10(1):12425.
PMID: 32709941
PMC: 7381616.
DOI: 10.1038/s41598-020-62446-5.
Is Phylotranscriptomics as Reliable as Phylogenomics?.
Cheon S, Zhang J, Park C
Mol Biol Evol. 2020; 37(12):3672-3683.
PMID: 32658973
PMC: 7743905.
DOI: 10.1093/molbev/msaa181.
Genomic Variations Underlying Speciation and Niche Specialization of .
Deng J, Auchtung J, Konstantinidis K, Brettar I, Hofle M, Tiedje J
mSystems. 2019; 4(5).
PMID: 31615877
PMC: 6794122.
DOI: 10.1128/mSystems.00560-19.
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone.
Cloutier A, Sackton T, Grayson P, Clamp M, Baker A, Edwards S
Syst Biol. 2019; 68(6):937-955.
PMID: 31135914
PMC: 6857515.
DOI: 10.1093/sysbio/syz019.
The synergistic effect of concatenation in phylogenomics: the case in .
Palmer M, Venter S, McTaggart A, Coetzee M, van Wyk S, Avontuur J
PeerJ. 2019; 7:e6698.
PMID: 31024760
PMC: 6474361.
DOI: 10.7717/peerj.6698.
Plant phylogenomics based on genome-partitioning strategies: Progress and prospects.
Yu X, Yang D, Guo C, Gao L
Plant Divers. 2019; 40(4):158-164.
PMID: 30740560
PMC: 6137260.
DOI: 10.1016/j.pld.2018.06.005.