Doh H, Lee C, Kim N, Park Y, Kim E, Choi C
Sci Rep. 2025; 15(1):5412.
PMID: 39948168
PMC: 11825734.
DOI: 10.1038/s41598-025-87719-9.
Fernando M, Fu J, Adamowicz S
Ecol Evol. 2025; 15(1):e70817.
PMID: 39781258
PMC: 11706799.
DOI: 10.1002/ece3.70817.
Xu S, Onoda A
J Mol Evol. 2024; 92(6):874-890.
PMID: 39636305
DOI: 10.1007/s00239-024-10215-7.
Morales P, Gajardo F, Valdivieso C, Valladares M, Di Genova A, Orellana A
BMC Genomics. 2024; 25(1):614.
PMID: 38890559
PMC: 11184842.
DOI: 10.1186/s12864-024-10416-w.
Kupperman M, Ke R, Leitner T
bioRxiv. 2023; .
PMID: 38076930
PMC: 10705478.
DOI: 10.1101/2023.11.30.567148.
Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations.
Combrink L, Humphreys I, Washburn Q, Arnold H, Stagaman K, Kasschau K
Front Microbiol. 2023; 14:1092216.
PMID: 36910202
PMC: 9992432.
DOI: 10.3389/fmicb.2023.1092216.
Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies.
Balbinott N, Rodrigues N, Guzman F, Turchetto-Zolet A, Margis R
Genet Mol Biol. 2022; 45(1):e20210191.
PMID: 35088818
PMC: 8796035.
DOI: 10.1590/1678-4685-GMB-2021-0191.
Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data.
Takezaki N
Genome Biol Evol. 2021; 13(5).
PMID: 33739405
PMC: 8103497.
DOI: 10.1093/gbe/evab052.
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.
Deciphering lignocellulose deconstruction by the white rot fungus based on genomic and transcriptomic analyses.
Qin X, Su X, Luo H, Ma R, Yao B, Ma F
Biotechnol Biofuels. 2018; 11:58.
PMID: 29507610
PMC: 5833081.
DOI: 10.1186/s13068-018-1060-9.
Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies.
Eyun S
BMC Evol Biol. 2017; 17(1):23.
PMID: 28103796
PMC: 5244711.
DOI: 10.1186/s12862-017-0883-5.
phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics.
Guy L
Bioinformatics. 2017; 33(8):1230-1232.
PMID: 28057682
PMC: 5408842.
DOI: 10.1093/bioinformatics/btw824.
PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.
Stephens T, Bhattacharya D, Ragan M, Chan C
PeerJ. 2016; 4:e2038.
PMID: 27190724
PMC: 4868591.
DOI: 10.7717/peerj.2038.
Mitochondrial data are not suitable for resolving placental mammal phylogeny.
Morgan C, Creevey C, OConnell M
Mamm Genome. 2014; 25(11-12):636-47.
PMID: 25239304
DOI: 10.1007/s00335-014-9544-9.
AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.
Zhou C, Mao F, Yin Y, Huang J, Gogarten J, Xu Y
PLoS One. 2014; 9(6):e98844.
PMID: 24892935
PMC: 4044049.
DOI: 10.1371/journal.pone.0098844.
Automated reconstruction of whole-genome phylogenies from short-sequence reads.
Bertels F, Silander O, Pachkov M, Rainey P, van Nimwegen E
Mol Biol Evol. 2014; 31(5):1077-88.
PMID: 24600054
PMC: 3995342.
DOI: 10.1093/molbev/msu088.
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees.
Misof B, Meyer B, von Reumont B, Kuck P, Misof K, Meusemann K
BMC Bioinformatics. 2013; 14:348.
PMID: 24299043
PMC: 3890606.
DOI: 10.1186/1471-2105-14-348.
Phylogenetic analysis of genome rearrangements among five mammalian orders.
Luo H, Arndt W, Zhang Y, Shi G, Alekseyev M, Tang J
Mol Phylogenet Evol. 2012; 65(3):871-82.
PMID: 22929217
PMC: 4425404.
DOI: 10.1016/j.ympev.2012.08.008.
Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
Wiens J, Tiu J
PLoS One. 2012; 7(8):e42925.
PMID: 22900065
PMC: 3416753.
DOI: 10.1371/journal.pone.0042925.
Molecular phylogeny and evolution of parabasalia with improved taxon sampling and new protein markers of actin and elongation factor-1α.
Noda S, Mantini C, Meloni D, Inoue J, Kitade O, Viscogliosi E
PLoS One. 2012; 7(1):e29938.
PMID: 22253832
PMC: 3253790.
DOI: 10.1371/journal.pone.0029938.