On reconstructing species trees from gene trees in term of duplications and losses
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Notung: dating gene duplications using gene family trees
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
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
An algorithm to enumerate all sorting reversals
Proceedings of the sixth annual international conference on Computational biology
Methods for reconstructing the history of tandem repeats and their application to the human genome
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
Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Reversal distance for partially ordered genomes
Bioinformatics
Inferring the Recent Duplication History of a Gene Cluster
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Evolution of tandemly arrayed genes in multiple species
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
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Given a phylogenetic tree T for a family of tandemly repeated genes and their signed order O on the chromosome, we aim to find the minimum number of inversions compatible with an evolutionary history of this family. This is the first attempt to account for inversions in an evolutionary model of tandemly repeated genes. We present a time-efficient branch-and-bound algorithm and show, using simulated data, that it can be used to detect “wrong” phylogenies among a set of putative ones for a given gene family. An application on a published phylogeny of KRAB zinc finger genes is presented.