Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa.
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[1] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[2] K. Kjer,et al. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. , 1995, Molecular phylogenetics and evolution.
[3] D. Ord,et al. PAUP:Phylogenetic analysis using parsi-mony , 1993 .
[4] J. Cracraft,et al. Parsimony and Phylogenetic Inference Using DNA Sequences : Some Methodological Strategies , 2022 .
[5] M S Waterman,et al. Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.
[6] Steffen Schulze-Kremer,et al. Molecular Bioinformatics: Algorithms and Applications , 1995 .
[7] A. K. Wong,et al. A survey of multiple sequence comparison methods. , 1992, Bulletin of mathematical biology.
[8] James F. Smith. Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .
[9] Mário C. C. Pinna. CONCEPTS AND TESTS OF HOMOLOGY IN THE CLADISTIC PARADIGM , 1991 .
[10] P. Stevens,et al. Homology and Phylogeny: Morphology and Systematics , 1984 .
[11] J. Devereux,et al. A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..
[12] J. Barta,et al. Phylogenetic analysis of the class Sporozoea (phylum Apicomplexa Levine, 1970): evidence for the independent evolution of heteroxenous life cycles. , 1989, The Journal of parasitology.
[13] M. Siddall,et al. Molecular phylogenetic evidence that the phylum Haplosporidia has an alveolate ancestry. , 1995, Molecular biology and evolution.
[14] Yves Van de Peer,et al. Database on the structure of small ribosomal subunit RNA , 1998, Nucleic Acids Res..
[15] R. Gutell,et al. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. , 1994, Microbiological reviews.
[16] J. Hein,et al. A tree reconstruction method that is economical in the number of pairwise comparisons used. , 1989, Molecular biology and evolution.
[17] B. Dalrymple,et al. Ribosomal DNA sequence comparison of Babesia and Theileria. , 1992, Molecular and biochemical parasitology.
[18] Masato Ishikawa,et al. Comprehensive study on iterative algorithms of multiple sequence alignment , 1995, Comput. Appl. Biosci..
[19] A. Smith. RNA SEQUENCE DATA IN PHYLOGENETIC RECONSTRUCTION: TESTING THE LIMITS OF ITS RESOLUTION , 1989, Cladistics : the international journal of the Willi Hennig Society.
[20] J Hein,et al. An algorithm combining DNA and protein alignment. , 1994, Journal of theoretical biology.
[21] S. Muse. Evolutionary analyses of DNA sequences subject to constraints of secondary structure. , 1995, Genetics.
[22] J. Corliss. An interim utilitarian [user-friendly] hierarchical classification and characterization of the protists , 1994 .
[23] S. Barker,et al. Phylogenetic position of the genus Perkinsus (Protista, Apicomplexa) based on small subunit ribosomal RNA. , 1993, Molecular and biochemical parasitology.
[24] F. Cox,et al. The evolutionary expansion of the Sporozoa. , 1994, International journal for parasitology.
[25] R DeSalle,et al. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. , 1993, Molecular phylogenetics and evolution.
[26] R F Doolittle,et al. Progressive alignment of amino acid sequences and construction of phylogenetic trees from them. , 1996, Methods in enzymology.
[27] G J Barton,et al. Evaluation and improvements in the automatic alignment of protein sequences. , 1987, Protein engineering.
[28] H Kishino,et al. Freeing phylogenies from artifacts of alignment. , 1992, Molecular biology and evolution.
[29] I. Rinsma-Melchert. The expected number of matches in optimal global sequence alignments , 1993 .
[30] R De Wachter,et al. DCSE, an interactive tool for sequence alignment and secondary structure research. , 1993, Computer applications in the biosciences : CABIOS.
[31] D. Penny,et al. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. , 1996, Molecular biology and evolution.
[32] F. Ayala,et al. Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[33] S. B. Needleman,et al. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 1989 .
[34] G. Olsen. Phylogenetic analysis using ribosomal RNA. , 1988, Methods in enzymology.
[35] M. Sleigh. Protozoa and other protists , 1989 .
[36] W. Wheeler,et al. MALIGN: A Multiple Sequence Alignment Program , 1994 .
[37] Ward C. Wheeler,et al. SEQUENCE ALIGNMENT, PARAMETER SENSITIVITY, AND THE PHYLOGENETIC ANALYSIS OF MOLECULAR DATA , 1995 .
[38] A. Johnson,et al. Phylogenetic relationships of Babesia divergens as determined from comparison of small subunit ribosomal RNA gene sequences. , 1994, Molecular and biochemical parasitology.
[39] J. Thompson,et al. Using CLUSTAL for multiple sequence alignments. , 1996, Methods in enzymology.
[40] Hideo Matsuda,et al. fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood , 1994, Comput. Appl. Biosci..
[41] G. Olsen,et al. Ribosomal RNA: a key to phylogeny , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[42] E J Milner-White,et al. Mix'n'Match: an improved multiple sequence alignment procedure for distantly related proteins using secondary structure predictions, designed to be independent of the choice of gap penalty and scoring matrix. , 1993, Protein engineering.
[43] N Takezaki,et al. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. , 1996, Molecular biology and evolution.
[44] Rupert De Wachter,et al. DCSE, an interactive tool for sequence alignment and secondary structure research , 1993, Comput. Appl. Biosci..
[45] J. Barta,et al. Evolutionary relationships of avian Eimeria species among other Apicomplexan protozoa: monophyly of the apicomplexa is supported. , 1991, Molecular biology and evolution.
[46] D. Hillis,et al. Ribosomal DNA: Molecular Evolution and Phylogenetic Inference , 1991, The Quarterly Review of Biology.
[47] W. Wheeler,et al. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. , 1988, Molecular biology and evolution.
[48] J. Wolters. The troublesome parasites--molecular and morphological evidence that Apicomplexa belong to the dinoflagellate-ciliate clade. , 1991, Bio Systems.
[49] D. Morrison. Phylogenetic tree-building. , 1996, International journal for parasitology.
[50] T. Smith,et al. Optimal sequence alignments. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[51] J. Baker. 2 – Systematics of Parasitic Protozoa , 1977 .
[52] S. Beverley,et al. Evolution of nuclear ribosomal RNAs in kinetoplastid protozoa: perspectives on the age and origins of parasitism. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[53] J. Huelsenbeck. Performance of Phylogenetic Methods in Simulation , 1995 .
[54] M. Sogin,et al. Ribosomal RNA sequences of Sarcocystis muris, Theileria annulata and Crypthecodinium cohnii reveal evolutionary relationships among apicomplexans, dinoflagellates, and ciliates. , 1991, Molecular and biochemical parasitology.
[55] J Hein,et al. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. , 1989, Molecular biology and evolution.
[56] W R Taylor,et al. Multiple protein sequence alignment: algorithms and gap insertion. , 1996, Methods in enzymology.
[57] M. P. Cummings,et al. Sampling properties of DNA sequence data in phylogenetic analysis. , 1995, Molecular biology and evolution.
[58] R. Doolittle. Molecular evolution: computer analysis of protein and nucleic acid sequences. , 1990, Methods in enzymology.
[59] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[60] A. Rodrigo,et al. Inadequate Support for an Evolutionary Link between the Metazoa and the Fungi , 1994 .
[61] M. Miyamoto,et al. Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method. , 1992, Molecular biology and evolution.
[62] W. Brown,et al. Rates and patterns of base change in the small subunit ribosomal RNA gene. , 1993, Genetics.
[63] M. A. McClure,et al. Comparative analysis of multiple protein-sequence alignment methods. , 1994, Molecular biology and evolution.
[64] T. Cavalier-smith,et al. Kingdom protozoa and its 18 phyla. , 1993, Microbiological reviews.
[65] A. Kluge,et al. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. , 1993, Molecular biology and evolution.
[66] M. Schlegel,et al. Protist evolution and phylogeny as discerned from small subunit ribosomal RNA sequence comparisons. , 1991, European journal of protistology.
[67] Anders Krogh,et al. Hidden Markov models for sequence analysis: extension and analysis of the basic method , 1996, Comput. Appl. Biosci..
[68] J. Hein. Unified approach to alignment and phylogenies. , 1990, Methods in enzymology.
[69] Yves Van de Peer,et al. Database on the structure of large ribosomal subunit RNA , 1994, Nucleic Acids Res..
[70] D. Hillis,et al. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. , 1993, Molecular biology and evolution.
[71] Yves Van de Peer,et al. TREECON: a software package for the construction and drawing of evolutionary trees , 1993, Comput. Appl. Biosci..
[72] C. M. Henneke,et al. A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites , 1989, Comput. Appl. Biosci..
[73] J A Lake,et al. The order of sequence alignment can bias the selection of tree topology. , 1991, Molecular biology and evolution.
[74] David M. Williams,et al. A NOTE OF MOLECULAR HOMOLOGY: MULTIPLE PATTERNS FROM SINGLE DATASETS , 1993, Cladistics : the international journal of the Willi Hennig Society.
[75] H. Tyson. Relationships between amino acid sequences determined through optimum alignments, clustering, and specific distance patterns: application to a group of scorpion toxins. , 1992, Genome.