PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

PLoS Computational Biology

Volumn 12, Issue 7, 2016, Pages

  Hanson Smith, Victor ^a   Johnson, Alexander ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; PORTALS; PROTEINS; USER INTERFACES; WEB SERVICES;

AMINO-ACIDS; EVOLUTIONARY RELATIONSHIPS; IN-VITRO; IN-VIVO; PHYLOGENETICS; PROTEIN FUNCTIONS; PROTEIN SEQUENCES; PROTEINS STRUCTURES; SEQUENCE RECONSTRUCTION; SEQUENCE STRUCTURE;

PHYLOGENETIC;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER INTERFACE; CONTROLLED STUDY; GENETIC DATABASE; MUTATIONAL ANALYSIS; PHYLOBOT DATABASE; PHYLOGENETIC TREE; PHYLOGENY; PLESIOMORPHY; SEQUENCE ALIGNMENT; THERMOSTABILITY; WEB BROWSER; ANIMAL; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; GENETICS; HUMAN; INTERNET; METABOLISM; MOLECULAR EVOLUTION; PROCEDURES; SOFTWARE;

PROTEIN;

ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENETICS; HUMANS; INTERNET; PHYLOGENY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84979978492     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004976     Document Type: Article

References (31)

1. Ortlund E, Bridgham JT, Redinbo MR, Thornton JW, Crystal structure of an ancient protein: evolution by conformational epistasis. Science2007, 317, 1544–8. 17702911
2. Bridgham J, Ortlund E, Thornton JW, Evolution of a New Function by Degenerative Mutation in Cephalochordate Steroid Receptors. PLoS Genetics2009, 4(9).
3. Baker CB, Hanson-Smith V, Johnson AD, Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science2013, 342, 104–8. doi: 10.1126/science.124081024092741
4. Howard C, Hanson-Smith V, Kennedy KJ, Miller C, Lou HJ, Johnson AJ, et al. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife2014, 3:e04126
5. McKeown A, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW, Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module. Cell2014, 159, 58–68. doi: 10.1016/j.cell.2014.09.00325259920
6. Kratzer JT, Lanaspa MA, Murphy MN, Cicerchi C, Graves CL, Tipton PA, et al. Evolutionary history and metabolic insights of ancient mammalian uricases. Proceeding of the National Academy of Sciences USA2014, 111(10), 3763–8.
7. Yang Z, Kumar S, Nei M, A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences. Genetics1995, 141, 1641–1650. 8601501
8. Thornton JW, Resurrecting Ancient Genes: Experimental Analysis of Extinct Molecules. Nature Reviews Genetics2004, 5, 366–75. 15143319
9. Harms MJ, Thornton JW, Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nature Reviews Genetics2013. 14(8), 559–571. doi: 10.1038/nrg354023864121
10. Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research2004, 32(5), 1792–97. 15034147
11. Liu Y, Schmidt B, Maskell DL, MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics2010, 26(16), 1958–64. doi: 10.1093/bioinformatics/btq33820576627
12. Price MN, Dehal PS, Arkin AP, (2010) FastTree 2 –Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. doi: 10.1371/journal.pone.000949020224823
13. Wu M, Chatterji S, Eisen JA, Accounting for alignment uncertainty in phylogenomics. PLoS One2012, 7, e30288, doi: 10.1371/journal.pone.003028822272325
14. Stamatakis A, Ludwig T, Meier H, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics2005, 21(4), 456–63. 15608047
15. Anisimova M, Gascuel O, . (2006) Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful alternative. Systematic Biology2006, 4, 539–552.
16. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology2010. 59(3). 307–321. doi: 10.1093/sysbio/syq01020525638
17. Hanson-Smith V, Kolaczkowski B, Thornton JM, Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty. Molecular Biology and Evolution2010, 27(9), 1988–99. doi: 10.1093/molbev/msq08120368266
18. Yang Z, PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution2007, 24(8), 1586–1591. 17483113
19. Sukumaran J, Holder MT, DendroPy: a Python library for phylogenetic computing. Bioinformatics2010, 26(12), 1569–71. doi: 10.1093/bioinformatics/btq22820421198
20. Edgar RC, Batzoglou S, Multiple Sequence Alignment. Current Opinion in Structural Biology2006, 16, 368–373. 16679011
21. Wong K, Suchard MA, Huelsenbeck JP, Alignment Uncertainty and Genomic Analysis. Science2008, 319, 416–17.
22. Felsenstein J, Inferring Phylogenies. Sinaur Associations, Inc.; 2004.
23. Yang Z, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution1994, 39(3), 306–14. 7932792
24. Lartillot N, Philippe H, A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution2004. 21(6), 1095–1109. 15014145
25. Akaike H, Information Theory and an Extension of the Maximum Likelihood Principle. Proceedings of the 2nd International Symposium on Information Theory1973, 267–81.
26. Abascal F, Zardoya R, Posada D, ProtTest: selection of best-fit models of protein evolution. Bioinformatics2005, 21, 2104–05. 15647292
27. Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O, Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes. Systematic Biology2011. 60(5), 685–699. doi: 10.1093/sysbio/syr04121540409
28. Fitch W, Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Systematic Zoology1971, 20(4), 406–16.
29. Williams PD, Pollock DD, Blackburne BP, Goldstein RA, Assessing the Accuracy of Ancestral Protein Reconstruction Methods. PLoS Computational Biology2006, 2(6), 598–604.
30. Harms MJ, Thornton JM, Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion Structural Biology2010, 20(3), 360–6.
31. Finnigan G, Hanson-Smith V, Stevens T, Thornton JW, Evolution of increased complexity in a molecular machine. Nature2012, 481, 360–4. doi: 10.1038/nature1072422230956