Inferring phylogenies of evolving sequences without multiple sequence alignment

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Chan, Cheong Xin ^a   Bernard, Guillaume ^a   Poirion, Olivier ^a,c   Hogan, James M ^b   Ragan, Mark A ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

^c ECOLE CENTRALE DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BIOLOGY; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOFTWARE;

AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84923334529     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep06504     Document Type: Article

References (64)

1. Edgar, R. C. & Batzoglou, S. Multiple sequence alignment. Curr. Opin. Struct. Biol. 16, 368-373 (2006).
2. Notredame, C. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput. Biol. 3, 1405-1408 (2007).
3. Darling, A. E., Miklos, I. & Ragan, M. A. Dynamics of genome rearrangement in bacterial populations. PLoS Genet. 4, e1000128 (2008).
4. Puigbò, P., Wolf, Y. I. & Koonin, E. V. The tree and net components of prokaryote evolution. Genome Biol. Evol. 2, 745-756 (2010).
5. Zhaxybayeva, O. & Doolittle, W. F. Lateral gene transfer. Curr. Biol. 21, R242-246 (2011).
6. Wong, K. M., Suchard, M. A. & Huelsenbeck, J. P. Alignment uncertainty and genomic analysis. Science 319, 473-476 (2008).
7. Wu, M. T., Chatterji, S. & Eisen, J. A. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7, e30288 (2012).
8. Chan, C. X. & Ragan, M. A. Next-generation phylogenomics. Biol. Direct 8, 3 (2013).
9. Höhl, M. & Ragan, M. A. Is multiple-sequence alignment required for accurate inference of phylogeny? Syst. Biol. 56, 206-221 (2007).
10. Höhl, M., Rigoutsos, I. & Ragan, M. A. Pattern-based phylogenetic distance estimation and tree reconstruction. Evol Bioinform Online 2, 359-375 (2006).
11. Domazet-Lošo, M. & Haubold, B. Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics 27, 1466-1472 (2011).
12. Vinga, S. & Almeida, J. Alignment-free sequence comparison - a review. Bioinformatics 19, 513-523 (2003).
13. Bonham-Carter, O., Steele, J. & Bastola, D. Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Brief. Bioinform., In Press, DOI:10.1093/bib/bbt052 (2013).
14. Haubold, B. Alignment-free phylogenetics and population genetics. Brief. Bioinform. 15, 407-418 (2014).
15. Song, K. et al. New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Brief. Bioinform. 15, 343-353 (2014).
16. Torney, D. C., Burks, C., Davison, D. & Sirotkin, K. M. in Computers and DNA - Santa Fe Institute Studies in the Sciences of Complexity, Vol. 7 (eds. Bell, G. & Marr, R.) 109-125 (Addison-Wesley, Reading, MA; 1990).
17. Wan, L., Reinert, G., Sun, F. & Waterman, M. S. Alignment-free sequence comparison (II): theoretical power of comparison statistics. J Comput. Biol. 17, 1467-1490 (2010).
18. Reinert, G., Chew, D., Sun, F. & Waterman, M. S. Alignment-free sequence comparison (I): statistics and power. J Comput. Biol. 16, 1615-1634 (2009).
19. 2, an algorithm for high-performance sequence comparison. J Comput. Biol. 1, 199-215 (1994).
20. Miller, R. T. et al. A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res. 9, 1143-1155 (1999).
21. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321 (2010).
22. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 - approximately maximumlikelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
23. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
24. Göke, J., Schulz, M. H., Lasserre, J. & Vingron, M. Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics 28, 656-663 (2012).
25. Yi, H. & Jin, L. Co-phylog: an assembly-free phylogenomic approach for closely related organisms. Nucleic Acids Res. 41, e75 (2013).
26. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
27. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542 (2012).
28. Robinson, D. F. & Foulds, L. R. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147 (1981).
29. Forêt, S., Wilson, S. R. & Burden, C. J. Empirical distribution of k-word matches in biological sequences. Pattern Recognit. 42, 539-548 (2009).
30. Forêt, S., Kantorovitz, M. R. & Burden, C. J. Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences. BMC Bioinformatics 7 Suppl 5, S21 (2006).
31. Huffman, D. A. A method for the construction of minimum-redundancy codes. Proc. IRE 40, 1098-1101 (1952).
32. Fletcher, W. & Yang, Z. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26, 1879-1888 (2009).
33. Lavalette, D. Facteur d'impact: impartialité ou impuissance? (INSERM U350 Institut Curie-Recherche, Bât. 112, Centre Universitaire, Orsay, France; 1996).
34. Popescu, I. I. On a Zipf's Law extension to impact factors. Glottometrics 6, 83-93 (2003).
35. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
36. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
37. Golubchik, T., Wise, M. J., Easteal, S. & Jermiin, L. S. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. Mol. Biol. Evol. 24, 2433-2442 (2007).
38. Kingman, J. F. C. The coalescent. Stoch. Proc. Appl. 13, 235-248 (1982).
39. Tellier, A. & Lemaire, C. Coalescence 2.0: a multiple branching of recent theoretical developments and their applications. Mol. Ecol. 23, 2637-2652 (2014).
40. Sjödin, P., Kaj, I., Krone, S., Lascoux, M. & Nordborg, M. On the meaning and existence of an effective population size. Genetics 169, 1061-1070 (2005).
41. Piel, W. H., Donoghue, M. J. & Sanderson, M. J. in To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceania. NIES Research Report, Vol. 171 (eds. Shimura, J., Wilson, K. L. & Gordon, D.) 41-47 (National Institute for Environmental Studies, Tsukuba, Japan; 2002).
42. Posada, D. Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J. Mol. Evol. 76, 351-352 (2013).
43. Ragan, M. A. & Chan, C. X. Biological intuition in alignment-free methods: response to Posada. J. Mol. Evol. 77, 1-2 (2013).
44. Ragan, M. A., Bernard, G. & Chan, C. X. Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra. RNA Biol. 11, 176-185 (2014).
45. Chan, C. X., Darling, A. E., Beiko, R. G. & Ragan, M. A. Are protein domains modules of lateral genetic transfer? PLoS ONE 4, e4524 (2009).
46. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
47. Thompson, J. D., Linard, B., Lecompte, O. & Poch, O. A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS ONE 6, e18093 (2011).
48. Liu, K., Linder, C. R. & Warnow, T. RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation. PLoS ONE 6, e27731 (2011).
49. Gunasinghe, U., Alahakoon, D. & Bedingfield, S. Extraction of high quality k words for alignment-free sequence comparison. J. Theor. Biol. 358, 31-51 (2014).
50. Haubold, B. & Pfaffelhuber, P. Alignment-free population genomics: an efficient estimator of sequence diversity. G3 2, 883-889 (2012).
51. Fitch, W. M. & Margoliash, E. Construction of phylogenetic trees. Science 155, 279-284 (1967).
52. Burden, C. J., Kantorovitz, M. R. & Wilson, S. R. Approximate word matches between two random sequences. Ann. Appl. Probab. 18, 1-21 (2008).
53. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
54. Tavaré, S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57-86 (1986).
55. Yang, Z. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39, 105-111 (1994).
56. Whelan, S. & Goldman, N. Ageneral empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691-699 (2001).
57. Arenas, M. & Posada, D. Coalescent simulation of intracodon recombination. Genetics 184, 429-437 (2010).
58. Sjöstrand, J., Arvestad, L., Lagergren, J. & Sennblad, B. GenPhyloData: realistic simulation of gene family evolution. BMC Bioinformatics 14, 209 (2013).
59. Drummond, A. J., Ho, S. Y., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).
60. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618 (2012).
61. Chan, C. X., Mahbob, M. & Ragan, M. A. Clustering evolving proteins into homologous families. BMC Bioinformatics 14, 120 (2013).
62. Stuart, G. W., Moffett, K. & Baker, S. Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics 18, 100-108 (2002).
63. Kupczok, A., Schmidt, H. & von Haeseler, A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol. Biol. 5, 37 (2010).
64. Bryant, D. & Steel, M. Computing the distribution of a tree metric. IEEE/ACM Trans. Comput. Biol. Bioinform. 6, 420-426 (2009).