Computational Biology and Applied Bioinformatics by Heitor Silverio Lopes - Leonardo Magalhães Cruz (Eds)

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By Heitor Silverio Lopes - Leonardo Magalhães Cruz (Eds)

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Henikoff, S. & Henikoff, J. (1992) Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the United States of America 89(22):10915. ; Taylor, W. & Thornton, J. (1994) A mutation data matrix for transmembrane proteins. FEBS Letters 339(3):269-275. Jukes, T. & Cantor, C. (1969) Evolution of protein molecules. ). Academic Press, New York. ; Okubo, K. & others. (2011). DDBJ progress report. ; Toh, H. & Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.

0. ), Atlas of protein sequence and structure 5:353-358. ; Vingron, M. & Von Haeseler A. (2002). TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18(3):502. ; Wu, G. & Kim, S. (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A 106(8):2677-82. Snir, S. & Tuller, T. (2009) The net-hmm approach: phylogenetic network inference by combining maximum likelihood and hidden Markov models.

Warnow, T. (2010) Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Currents 2. ; Zhang, A. & Zhu, C. (2010) Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evolutionary Biology 10(1):242. ; Dress, A. & Werner, T. (1998). DIALIGN: finding local similarities by multiple sequence alignment. Bionformatics 14:290 - 294 Needleman, S. & Wunsch, C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins.

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