Co-phylog: An assembly-free phylogenomic approach for closely related organisms

Nucleic Acids Research

Volumn 41, Issue 7, 2013, Pages

  Yi, Huiguang ^a   Jin, Li ^a,b  

^a FUDAN UNIVERSITY   (China)

^b Fudan Taizhou Institute of Health Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; HIGH THROUGHPUT SEQUENCING; INTERMETHOD COMPARISON; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENOMICS; PRIORITY JOURNAL; SIMULATION;

ALGORITHMS; COMPUTER SIMULATION; ENTEROBACTERIACEAE; ESCHERICHIA; GAMMAPROTEOBACTERIA; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PHYLOGENY; SEQUENCE ALIGNMENT; SHIGELLA; SOFTWARE;

EID: 84876526790     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt003     Document Type: Article

References (32)

1. Wiens, J.J. (2003) Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol., 52, 528-538. (Pubitemid 36990380)
2. Snel, B., Bork, P. and Huynen, M.A. (1999) Genome phylogeny based on gene content. Nat. Genet., 21, 108-110. (Pubitemid 29036294)
3. Blanchette, M., Kunisawa, T. and Sankoff, D. (1999) Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol., 49, 193-203. (Pubitemid 29357862)
4. Ulitsky, I., Burstein, D., Tuller, T. and Chor, B. (2006) The average common substring approach to phylogenomic reconstruction. J. Comput. Biol., 13, 336-350.
5. Qi, J., Wang, B. and Hao, B.I. (2004) Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J. Mol. Evol., 58, 1-11. (Pubitemid 38120400)
6. Hohl, M. and Ragan, M.A. (2007) Is multiple-sequence alignment required for accurate inference of phylogeny? Syst. Biol., 56, 206-221.
7. Loytynoja, A. and Goldman, N. (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320, 1632-1635. (Pubitemid 351931252)
8. Wong, K.M., Suchard, M.A. and Huelsenbeck, J.P. (2008) Alignment uncertainty and genomic analysis. Science, 319, 473-476. (Pubitemid 351160582)
9. Elias, I. (2006) Settling the intractability of multiple alignment. J. Comput. Biol., 13, 1323-1339. (Pubitemid 46100696)
10. Wang, L. and Jiang, T. (1994) On the complexity of multiple sequence alignment. J. Comput. Biol., 1, 337-348.
11. Stuart, G.W. and Berry, M.W. (2003) A comprehensive whole genome bacterial phylogeny using correlated peptide motifs defined in a high dimensional vector space. J. Bioinform. Comput. Biol., 1, 475-493.
12. Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P. and Zhang, H. (2001) An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 17, 149-154. (Pubitemid 32208523)
13. Chen, X., Kwong, S. and Li, M. (1999) A compression algorithm for DNA sequences and its applications in genome comparison. Genome Inform. Ser. Workshop Genome Inform., 10, 51-61.
14. Otu, H.H. and Sayood, K. (2003) A new sequence distance measure for phylogenetic tree construction. Bioinformatics, 19, 2122-2130. (Pubitemid 37408164)
15. Jun, S.R., Sims, G.E., Wu, G.A. and Kim, S.H. (2010) Whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution. Proc. Natl. Acad. Sci. USA, 107, 133-138.
16. Cannon, C.H., Kua, C.S., Zhang, D. and Harting, J.R. (2010) Assembly free comparative genomics of short-read sequence data discovers the needles in the haystack. Mol. Ecol., 19(Suppl. 1), 147-161.
17. Ratan, A., Zhang, Y., Hayes, V.M., Schuster, S.C. and Miller, W. (2010) Calling SNPs without a reference sequence. BMC Bioinformatics, 11, 130.
18. Peterlongo, P., Schnel, N., Nadia, P., Sagot, M.-F. and Vincent, L. (2010) Identifying SNPs without a reference genome by comparing raw reads. In: Chavez, E. and Lonardi, S. (eds), String Processing and Information Retrieval-17th International Symposium, Vol. 6393. Los Cabos, Mexico, pp. 147-158.
19. Ma, B., Tromp, J. and Li, M. (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics, 18, 440-445. (Pubitemid 34284945)
20. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
21. Foster, J.T., Beckstrom-Sternberg, S.M., Pearson, T., Beckstrom-Sternberg, J.S., Chain, P.S., Roberto, F.F., Hnath, J., Brettin, T. and Keim, P. (2009) Whole-genome-based phylogeny and divergence of the genus Brucella. J. Bacteriol., 191, 2864-2870.
22. Domazet-Loso, M. and Haubold, B. (2009) Efficient estimation of pairwise distances between genomes. Bioinformatics, 25, 3221-3227.
23. Zhou, Z., Li, X., Liu, B., Beutin, L., Xu, J., Ren, Y., Feng, L., Lan, R., Reeves, P.R. and Wang, L. (2010) Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One, 5, e8700.
24. Darling, A.E., Mau, B. and Perna, N.T. (2010) ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5, e11147.
25. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, D141-D145.
26. Dalquen, D.A., Anisimova, M., Gonnet, G.H. and Dessimoz, C. (2012) ALF- A simulation framework for genome evolution. Mol. Biol. Evol., 29, 1115-1123.
27. Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, E., Bonacorsi, S., Bouchier, C., Bouvet, O. et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet., 5, e1000344.
28. Wagner, A. and de la Chaux, N. (2008) Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Mol. Genet. Genomics, 280, 397-408.
29. Huang, W., Li, L., Myers, J.R. and Marth, G.T. (2012) ART: a next-generation sequencing read simulator. Bioinformatics, 28, 593-594.
30. Glenn, T.C. (2011) Field guide to next-generation DNA sequencers. Mol. Ecol. Resour., 11, 759-769.
31. Hu, X., Yuan, J., Shi, Y., Lu, J., Liu, B., Li, Z., Chen, Y., Mu, D., Zhang, H., Li, N. et al. (2012) pIRS: profile-based Illumina pair-end reads simulator. Bioinformatics, 28, 1533-1535.
32. Edgar, R.C. (2004) Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res., 32, 380-385. (Pubitemid 38228638)