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Concept

Cladistics

Related publications (28)

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Yu Lin, Vaibhav Rajan

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

2011

Comparing COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida)

Enrique Lara

The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal “DNA barcode” for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses h ...

2011

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Bernard Moret, Xiuwei Zhang

Background: Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the inference of regulatory networks for ...

2010

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Yu Lin, Vaibhav Rajan

Springer2010

On Exploring Genome Rearrangement Phylogenetic Patterns

The study of genorne rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed ...

Springer-Verlag New York2010

How many bootstrap replicates are necessary?

Bernard Moret, Alexandros Stamatakis

Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reco ...

2010

Improving inference of transcriptional regulatory networks based on network evolutionary models

Bernard Moret, Xiuwei Zhang

Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the inference of regulatory networks for a family of ...

Springer2009

Maximum independent sets of commuting and noninterfering inversions

Bernard Moret, Krister Swenson

Background: Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard to approximate. Yet median-based ap ...

2009