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. Maximum parsimony for tree mixtures. Grünewald S; Moulton V IEEE/ACM Trans Comput Biol Bioinform; 2009; 6(1):97-102. PubMed ID: 19179702 [TBL] [Abstract][Full Text] [Related]
4. Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction. Ané C Genome Biol Evol; 2011; 3():246-58. PubMed ID: 21362638 [TBL] [Abstract][Full Text] [Related]
5. The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. McCann A; Cotton JA; McInerney JO BMC Evol Biol; 2008 Nov; 8():312. PubMed ID: 19014489 [TBL] [Abstract][Full Text] [Related]
6. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. Walker JF; Yang Y; Feng T; Timoneda A; Mikenas J; Hutchison V; Edwards C; Wang N; Ahluwalia S; Olivieri J; Walker-Hale N; Majure LC; Puente R; Kadereit G; Lauterbach M; Eggli U; Flores-Olvera H; Ochoterena H; Brockington SF; Moore MJ; Smith SA Am J Bot; 2018 Mar; 105(3):446-462. PubMed ID: 29738076 [TBL] [Abstract][Full Text] [Related]
7. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Rasmussen MD; Kellis M Genome Res; 2007 Dec; 17(12):1932-42. PubMed ID: 17989260 [TBL] [Abstract][Full Text] [Related]
8. Bayesian coestimation of phylogeny and sequence alignment. Lunter G; Miklós I; Drummond A; Jensen JL; Hein J BMC Bioinformatics; 2005 Apr; 6():83. PubMed ID: 15804354 [TBL] [Abstract][Full Text] [Related]
9. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. Zmasek CM; Eddy SR BMC Bioinformatics; 2002 May; 3():14. PubMed ID: 12028595 [TBL] [Abstract][Full Text] [Related]
10. Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences. Bernt M; Braband A; Middendorf M; Misof B; Rota-Stabelli O; Stadler PF Mol Phylogenet Evol; 2013 Nov; 69(2):320-7. PubMed ID: 23023207 [TBL] [Abstract][Full Text] [Related]
12. Discordance of species trees with their most likely gene trees. Degnan JH; Rosenberg NA PLoS Genet; 2006 May; 2(5):e68. PubMed ID: 16733550 [TBL] [Abstract][Full Text] [Related]
13. Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets. Nagy LG; Szöllősi G Adv Genet; 2017; 100():49-72. PubMed ID: 29153404 [TBL] [Abstract][Full Text] [Related]
14. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Podell S; Gaasterland T Genome Biol; 2007; 8(2):R16. PubMed ID: 17274820 [TBL] [Abstract][Full Text] [Related]
15. Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons. Shi CM; Yang Z Mol Biol Evol; 2018 Jan; 35(1):159-179. PubMed ID: 29087487 [TBL] [Abstract][Full Text] [Related]
16. Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits. Delaye L; Vargas C; Latorre A; Moya A Methods Mol Biol; 2020; 2075():355-369. PubMed ID: 31584175 [TBL] [Abstract][Full Text] [Related]
17. The quest for orthologs: finding the corresponding gene across genomes. Kuzniar A; van Ham RC; Pongor S; Leunissen JA Trends Genet; 2008 Nov; 24(11):539-51. PubMed ID: 18819722 [TBL] [Abstract][Full Text] [Related]
19. Genome trees and the tree of life. Wolf YI; Rogozin IB; Grishin NV; Koonin EV Trends Genet; 2002 Sep; 18(9):472-9. PubMed ID: 12175808 [TBL] [Abstract][Full Text] [Related]
20. Phylogenetic Analysis of Protein Family. Song L; Wu S; Tsang A Methods Mol Biol; 2018; 1775():267-275. PubMed ID: 29876824 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]