Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
SIAM Journal on Computing
Zinc finger gene clusters and tandem gene duplication
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
From Gene Trees to Species Trees
SIAM Journal on Computing
Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
Reconstructing the Duplication History of a Tandem Repeat
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
INFORMS Journal on Computing
Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring a duplication, speciation and loss history from a gene tree
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Evolution of tandemly repeated sequences through duplication and inversion
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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Tandemly arrayed genes (TAG) constitute a large fraction of most genomes and play important biological roles. They evolve through unequal recombination, which places duplicated genes next to the original ones (tandem duplications). Many algorithms have been proposed to infer a tandem duplication history for a TAG cluster in a single species. However, the presence of different transcriptional orientations in most TAG clusters highlight the fact that processes such as inversions also contribute to their evolution. This makes those algorithms unsuitable in many cases. To circumvent this limitation, we proposed in a previous work an extended evolutionary model which includes inversions and presented a branch-and-bound algorithm allowing to infer a most parsimonious scenario of evolution for a given TAG cluster. Here, we generalize this model to multiple species and present a general framework to infer ancestral gene orders that minimize the number of inversions in the whole evolutionary history. An application on a pair of human-rat TAG clusters is presented.