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Rate Matrices for Analyzing Large Families of Protein Sequences
Journal of Computational Biology
We propose and study a new approach for the analysis of families of protein sequences. This method is related to the LogDet distances used in phylogenetic reconstructions; it can be viewed as an attempt to embed these distances into a multi-dimensional framework. The proposed method starts by associating a Markov matrix to each pairwise alignments deduced from a given multiple alignment. The central objects under consideration here are matrix-valued logarithms L of these Markov matrices, whichdoi:10.1089/106652701752236205 pmid:11571074 fatcat:doquwcwvirbpjj7vi7dqfagnia