Detecting distant homologs using phylogenetic tree‐based HMMs
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[1] Richard A. Goldstein,et al. Probabilistic reconstruction of ancestral protein sequences , 1996, Journal of Molecular Evolution.
[2] L. Cavalli-Sforza,et al. PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES , 1967, Evolution; international journal of organic evolution.
[3] M Vingron,et al. Phylogenetic information improves homology detection , 2001, Proteins.
[4] D. Lipman,et al. Extracting protein alignment models from the sequence database. , 1997, Nucleic acids research.
[5] A. D. McLachlan,et al. Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[6] KharHengChoo,et al. Recent Applications of Hidden Markov Models in Computational Biology , 2004 .
[7] Kevin Karplus,et al. A Flexible Motif Search Technique Based on Generalized Profiles , 1996, Comput. Chem..
[8] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[9] Patrice Koehl,et al. ASTRAL compendium enhancements , 2002, Nucleic Acids Res..
[10] A. Bairoch. PROSITE: a dictionary of sites and patterns in proteins. , 1991, Nucleic acids research.
[11] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[12] P E Bourne,et al. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.
[13] Ziheng Yang,et al. Phylogenetic Analysis by Maximum Likelihood (PAML) , 2002 .
[14] S. Eddy. Hidden Markov models. , 1996, Current opinion in structural biology.
[15] Kevin Karplus,et al. A ?ex-ible search technique based on generalized profiles , 1996 .
[16] D. Haussler,et al. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.
[17] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[18] William H. Press,et al. Numerical recipes in C , 2002 .
[19] G. Mitchison. A Probabilistic Treatment of Phylogeny and Sequence Alignment , 1999, Journal of Molecular Evolution.
[20] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[21] Matthew W. Dimmic,et al. Modeling evolution at the protein level using an adjustable amino acid fitness model. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[22] J. Adachi,et al. MOLPHY version 2.3 : programs for molecular phylogenetics based on maximum likelihood , 1996 .
[23] C. Chothia,et al. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[24] Ian Holmes,et al. Evolutionary HMMs: a Bayesian approach to multiple alignment , 2001, Bioinform..
[25] W. Bruno. Modeling residue usage in aligned protein sequences via maximum likelihood. , 1996, Molecular biology and evolution.
[26] William Noble Grundy,et al. Homology Detection via Family Pairwise Search , 1998, J. Comput. Biol..
[27] Amos Bairoch,et al. The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..
[28] R. Durbin,et al. Tree-based maximal likelihood substitution matrices and hidden Markov models , 1995, Journal of Molecular Evolution.
[29] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[30] Richard Hughey,et al. Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..
[31] D. Higgins,et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.
[32] J. Felsenstein,et al. An evolutionary model for maximum likelihood alignment of DNA sequences , 1991, Journal of Molecular Evolution.
[33] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[34] S. Whelan,et al. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.
[35] Walter M. Fitch,et al. On the Problem of Discovering the Most Parsimonious Tree , 1977, The American Naturalist.