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Comparison of Tree-Child Phylogenetic Networks
- Gabriel Cardona, F. Rosselló, G. Valiente
- BiologyIEEE/ACM Transactions on Computational Biology…
- 27 August 2007
An injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors are provided, and this representation is used to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class.
A new balance index for phylogenetic trees
Diffusional conductances to CO2 as a target for increasing photosynthesis and photosynthetic water-use efficiency
It is suggested that the appropriate trait for selection for enhanced WUE is increased gm/gs, and it is concluded that for simultaneous improvement of AN and WUE, genetic manipulation of gm should avoid parallel changes in gs.
Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf
- Gabriel Cardona, A. Mir, F. Rosselló, Lucía Rotger, David Sánchez
- BiologyBMC Bioinformatics
- 16 January 2013
The cophenetic metrics can be safely used on weighted phylogenetic trees with nested taxa and no restriction on degrees, and they can be computed in O(n2) time, where n stands for the number of taxa.
Marvel Universe looks almost like a real social network
We investigate the structure of the Marvel Universe collaboration network, where two Marvel characters are considered linked if they jointly appear in the same Marvel comic book. We show that this…
On the coverings by tolerance classes
Extended Newick: it is time for a standard representation of phylogenetic networks
The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetics networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.
The mean value of the squared path-difference distance for rooted phylogenetic trees
A distance metric for a class of tree-sibling phylogenetic networks
A distance measure on the class of semi-binary tree-sibling time consistent phylogenetic networks, which generalize tree-child time consistent evolutionary networks, and thus also galled-trees, which can be computed in polynomial time by means of simple algorithms.
Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric
- Gabriel Cardona, M. Llabrés, F. Rosselló, G. Valiente
- Computer ScienceIEEE/ACM Transactions on Computational Biology…
This paper studies three metrics that have already been introduced in the literature: the Robinson-Foulds distance, the tripartition distance, and the mu-distance, and obtains tight bounds on the size of a tree-child time-consistent phylogenetic network.