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The construction of evolutionary trees is a fundamental problem in biology, and yet methods for reconstructing evolutionary trees are not reliable when it comes to inferring accurate topologies of large divergent evolutionary trees from realistic length sequences. We address this problem and present a new polynomial time algorithm for reconstructing evolutionary trees called the Short Quartets Method...
Inferring evolutionary trees is an interesting and important problem in biology, but one that is computationally difficult as most associated optimization problems are NP-hard. Although many methods are provably statistically consistent (i.e. the probability of recovering the correct tree converges to 1 as the sequence length increases), the actual rate of convergence for different methods has not...
We investigate the evolutionary relationships between photosynthetic reaction center proteins (D1, D2, L and M) and demonstrate that the pattern of nucleotide substitution in these is more complicated than has been assumed in previous phylogenetic analyses. We show that there are serious violations of methodological assumptions in previous published studies. We conclude that there is equal support...
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