Simultaneous phylogeny reconstruction and multiple sequence alignment

BMC Bioinformatics

Volumn 10, Issue SUPPL. 1, 2009, Pages

  Yue, Feng ^a   Shi, Jian ^b   Tang, Jijun ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of South Carolina   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX SUBSTITUTIONS; EVOLUTIONARY HISTORY; MULTIPLE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; MULTIPLE SEQUENCES; PHYLOGENETIC RECONSTRUCTION; PHYLOGENETIC TREES; PHYLOGENY RECONSTRUCTION;

ALGORITHMS; EXPERIMENTS; SOFTWARE PACKAGES; BIOINFORMATICS;

BIOLOGY;

ALGORITHM; ARTICLE; DNA SEQUENCE; GENETIC DATABASE; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

EID: 60849092251     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S11     Document Type: Article

References (32)

1. Higgins D Sharp P CLUSTAL: A package for performing multiple sequence alignment on a microcomputer Gene 1988, 73:237-244 3243435
2. Thompson J Higgins D Gibson T CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice Nucleic Acids Research 1994, 22(22):4673-4690 308517 7984417
3. Notredame C Recent progress in multiple sequence alignment: A survey Pharmacogenomics 2002, 3:131-144 11966409
4. Notredame C Higgins D Heringa J T-Coffee: A novel method for fast and accurate multiple sequence alignment J Mol Biol 2000, 302:205-217 10964570
5. Roshan U Livesay D Chikkagoudar S Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees Proc. 6th IEEE Symposium on BionInformatics and BioEngineering (BIBE) 2006:159-164
6. Wong K Suchard M Huelsenbeck J Alignment uncertainty and genomic analysis Science 2008, 319(5862):473-476 18218900
7. Goldman N Effects of sequence alignment procedures on estimates of phylogeny BioEssays 1998, 20(4):287-290
8. Varon A Vinh L Bomash I Wheeler W POY (Phylogenetic analysis of DNA and other data using dynamic homology) American Museum of Natural History http://research.amnh.org/scicomp/projects/poy.php
9. Ogden T Rosenberg M Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP* Syst Biol 2007, 56(2):182-193 17454974
10. Strugnell J Nishiguchi M Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: A comparison of alignment, implied alignment and analysis methods Journal Molluscan Studies 2007, 73(4):399-41
11. Vingron M Haeseler A Towards integration of multiple alignment and phylogenetic tree construction J Comp Biol 1997, 4:23-34
12. Sankoff D Minimal mutation trees of sequences SIAM J on App Math 1975, 28:35-42
13. Wang L Jiang T On the complexity of multiple sequence alignment J Comp Biol 1994, 1(4):337-348
14. Jiang T Liu F Tree alignment and reconstruction application software 1996
15. Lancia G Ravi R GESTALT: Genomic steiner alignments Proc. 10th Annual Symposium on Combinatorial Pattern Matching (CPM) 1999:101-114
16. Hein J A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given Mol Biol Evol 1989, 6(6):649-668 2488477
17. Saitou N Nei M The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol Biol Evol 1987, 4(4):406-425 3447015
18. Sankoff D Cedergren R Lapalme G Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA J Mol Evol 1976, 7(2):133-149 772222
19. Gotoh O Alignment of three biological sequences with an efficient traceback procedure J Theo Biol 1986, 121(3):327-337
20. Powell D Allison L Dix T Fast, optimal alignment of three sequences using linear gap costs J Theo Biol 2000, 207(3):325-336
21. Pearson W Rapid and sensitive sequence comparison with FASTP and FASTA Methods in Enzymology 1990, 183:63-98 2156132
22. Henikoff S Henikoff J Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 1992, 89(22):10915-10919 50453 1438297
23. Yue F Tang J A divide-and-conquer implementation of three sequence alignment and ancestor inference Proc. 1st IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2007:143-150
24. Myers E Miller W Optimal alignments in linear space Computer Applications in the Biosciences 1988, 4:11-17 3382986
25. Sankoff D Blanchette M Multiple genome rearrangement and breakpoint phylogeny J Comput Biol 1998, 5(3):555-570 9773350
26. Moret BME Wyman S Bader DA Warnow T Yan M A new implementation and detailed study of breakpoint analysis Proc. 6th Pacific Symp. Biocomputing (PSB) 2001:583-594
27. Huson D Nettles S Warnow T Disk-covering, a fast converging method for phylogenetic tree reconstruction. J Comput Biol 1999, 6(3):369-386
28. Stoye J Evers D Meyer F Rose: Generating sequence families Bioinformatics 1998, 14(2):157-163 9545448
29. Robinson R Foulds L Comparison of phylogenetic trees Mathematical Biosciences 1981, 53:131-147
30. Swofford D PAUP*: Phylogenetic analysis using parsimony (and other methods), ver 4.0 Sinauer Associates, Sunderland, Massachusetts
31. Sanderson M r8s software package http://ginger.ucdavis.edu/r8s
32. Thompson J Plewniak F Poch O BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs Bioinformatics 1999, 15:87-88 10068696