These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
3. JCoDA: a tool for detecting evolutionary selection. Steinway SN; Dannenfelser R; Laucius CD; Hayes JE; Nayak S BMC Bioinformatics; 2010 May; 11():284. PubMed ID: 20507581 [TBL] [Abstract][Full Text] [Related]
4. Beginner's Guide on the Use of PAML to Detect Positive Selection. Álvarez-Carretero S; Kapli P; Yang Z Mol Biol Evol; 2023 Apr; 40(4):. PubMed ID: 37096789 [TBL] [Abstract][Full Text] [Related]
6. Optimization strategies for fast detection of positive selection on phylogenetic trees. Valle M; Schabauer H; Pacher C; Stockinger H; Stamatakis A; Robinson-Rechavi M; Salamin N Bioinformatics; 2014 Apr; 30(8):1129-1137. PubMed ID: 24389654 [TBL] [Abstract][Full Text] [Related]
7. Maximum-likelihood approaches reveal signatures of positive selection in IL genes in mammals. Neves F; Abrantes J; Steinke JW; Esteves PJ Innate Immun; 2014 Feb; 20(2):184-91. PubMed ID: 23775092 [TBL] [Abstract][Full Text] [Related]
8. Inference of Episodic Changes in Natural Selection Acting on Protein Coding Sequences via CODEML. Bielawski JP; Baker JL; Mingrone J Curr Protoc Bioinformatics; 2016 Jun; 54():6.15.1-6.15.32. PubMed ID: 27322407 [TBL] [Abstract][Full Text] [Related]
9. PoSE: visualization of patterns of sequence evolution using PAML and MATLAB. Zhao K; Henderson E; Bullard K; Oberste MS; Burns CC; Jorba J BMC Bioinformatics; 2018 Oct; 19(Suppl 11):364. PubMed ID: 30343671 [TBL] [Abstract][Full Text] [Related]
10. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Jeffares DC; Tomiczek B; Sojo V; dos Reis M Methods Mol Biol; 2015; 1201():65-90. PubMed ID: 25388108 [TBL] [Abstract][Full Text] [Related]
11. EasyCodeML: A visual tool for analysis of selection using CodeML. Gao F; Chen C; Arab DA; Du Z; He Y; Ho SYW Ecol Evol; 2019 Apr; 9(7):3891-3898. PubMed ID: 31015974 [TBL] [Abstract][Full Text] [Related]
12. PAML 4: phylogenetic analysis by maximum likelihood. Yang Z Mol Biol Evol; 2007 Aug; 24(8):1586-91. PubMed ID: 17483113 [TBL] [Abstract][Full Text] [Related]
13. EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A. Ndhlovu A; Durand PM; Hazelhurst S Database (Oxford); 2015; 2015():bav065. PubMed ID: 26140928 [TBL] [Abstract][Full Text] [Related]
14. PAMLX: a graphical user interface for PAML. Xu B; Yang Z Mol Biol Evol; 2013 Dec; 30(12):2723-4. PubMed ID: 24105918 [TBL] [Abstract][Full Text] [Related]
15. Measuring Natural Selection. da Silva AG Methods Mol Biol; 2017; 1525():315-347. PubMed ID: 27896727 [TBL] [Abstract][Full Text] [Related]
16. Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nickel GC; Tefft D; Adams MD Nucleic Acids Res; 2008 Jan; 36(Database issue):D800-8. PubMed ID: 17962310 [TBL] [Abstract][Full Text] [Related]
17. Detecting the signatures of adaptive evolution in protein-coding genes. Bielawski JP Curr Protoc Mol Biol; 2013 Jan; Chapter 19():Unit 19.1.. PubMed ID: 23288462 [TBL] [Abstract][Full Text] [Related]
19. Genome-wide analysis of MAPKKKs shows expansion and evolution of a new MEKK class involved in solanaceous species sexual reproduction. Daigle C; Matton DP BMC Genomics; 2015 Dec; 16():1037. PubMed ID: 26645086 [TBL] [Abstract][Full Text] [Related]