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HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.
Mol Biol Evol. 2020 Jan 1;37(1):295-299. doi: 10.1093/molbev/msz197.
2
HyPhy: hypothesis testing using phylogenies.
Bioinformatics. 2005 Mar 1;21(5):676-9. doi: 10.1093/bioinformatics/bti079. Epub 2004 Oct 27.
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Relative evolutionary rate inference in HyPhy with LEISR.
PeerJ. 2018 Feb 5;6:e4339. doi: 10.7717/peerj.4339. eCollection 2018.
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Detecting Amino Acid Coevolution with Bayesian Graphical Models.
Methods Mol Biol. 2019;1851:105-122. doi: 10.1007/978-1-4939-8736-8_6.
6
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.
Bioinformatics. 2012 Oct 15;28(20):2685-6. doi: 10.1093/bioinformatics/bts507. Epub 2012 Aug 24.
7
Robust inference of positive selection from recombining coding sequences.
Bioinformatics. 2006 Oct 15;22(20):2493-9. doi: 10.1093/bioinformatics/btl427. Epub 2006 Aug 7.
8
Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes.
PLoS One. 2021 Mar 12;16(3):e0248337. doi: 10.1371/journal.pone.0248337. eCollection 2021.
10
paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences.
Genes (Basel). 2022 Jun 18;13(6):1090. doi: 10.3390/genes13061090.

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TCR germline diversity reveals evidence of natural selection on variable and joining alpha chain genes.
bioRxiv. 2025 Aug 24:2025.08.20.671277. doi: 10.1101/2025.08.20.671277.
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Positive selection at core genes may underlie niche adaptation in Fusobacterium animalis.
Gut Pathog. 2025 Aug 11;17(1):61. doi: 10.1186/s13099-025-00740-1.
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Positive Selection Drives Mitochondrial Gene Rearrangement in Sternorrhyncha (Insecta: Hemiptera).
Ecol Evol. 2025 Jul 20;15(7):e71789. doi: 10.1002/ece3.71789. eCollection 2025 Jul.
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EpiMolBio: A novel user-friendly bioinformatic program for genetic variability analysis.
Comput Struct Biotechnol J. 2025 Jun 26;27:2968-2975. doi: 10.1016/j.csbj.2025.06.034. eCollection 2025.
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Widespread variation in is associated with diverse melanin loss phenotypes across avian species.
bioRxiv. 2025 Jun 14:2025.06.13.659395. doi: 10.1101/2025.06.13.659395.

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2
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. eCollection 2019 Apr.
3
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7.
4
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549. doi: 10.1093/molbev/msy096.
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Cloud computing for genomic data analysis and collaboration.
Nat Rev Genet. 2018 May;19(5):325. doi: 10.1038/nrg.2018.8. Epub 2018 Feb 12.
6
Relative evolutionary rate inference in HyPhy with LEISR.
PeerJ. 2018 Feb 5;6:e4339. doi: 10.7717/peerj.4339. eCollection 2018.
7
The State of Software for Evolutionary Biology.
Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014.
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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
Syst Biol. 2016 Jul;65(4):726-36. doi: 10.1093/sysbio/syw021. Epub 2016 May 28.
10
Gene-wide identification of episodic selection.
Mol Biol Evol. 2015 May;32(5):1365-71. doi: 10.1093/molbev/msv035. Epub 2015 Feb 19.

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