Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees
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A set of phylogenetic trees with overlapping leaf sets is consistent if it can be merged without conflicts into a supertree. In this paper, we study the polynomial-time approximability of two related optimization problems called the maximum rooted triplets ...
A gene encoding a protein kinase was identified by homology-based PCR amplification in Encephalitozoon intestinalis, a microsporidian parasite pathogenic to humans, and its orthologue has been identified by database mining in the genome of the related spec ...
Motivation: Phylogenetic reconstruction from gene-order data has attracted increasing attention from both biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods (such as neighbor-joining), ...
To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphologica ...
We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Our mathematical techniques include new polynomial-time methods for bounding the inversion length of a candidate tree and new polynomial-time methods for estimat ...
We consider the problem of correlated data gathering by a network with a sink node and a tree based communication structure, where the goal is to minimize the total trans- mission cost of transporting the information collected by the nodes, to the sink nod ...
Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far ...
We report on our progress in reconstructing phylogenies from gene-order data. We have developed polynomial-time methods for estimating genomic distances that greatly improve the accuracy of trees obtained using the popular neighbor-joining method; we have ...
Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap su ...
Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in ...