MLGO: phylogeny reconstruction and ancestral inference from gene-order data
نویسندگان
چکیده
منابع مشابه
Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny
Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiosperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, includ...
متن کاملInternal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny
Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiopsperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, inclu...
متن کاملAdvances in phylogeny reconstruction from gene order and content data.
Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systematists for inferring deep evolutionary histories. This chapter surveys recent developmen...
متن کاملInversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
Phylogeny reconstruction from gene-order data has attracted much attention over the last few years. The two software packages used for that purpose, BPAnalysis and GRAPPA, both use so-called breakpoint medians in their computations. Some of our past results indicate that using inversion scores rather than breakpoint scores in evaluating trees leads to the selection of better trees. On that basi...
متن کاملAn Improved Algorithm for Ancestral Gene Order Reconstruction
Genome rearrangements are large-scale mutations that change the order and orientation of genes in genomes. In the small phylogeny problem, we are given gene orders in several current species and a phylogenetic tree representing their evolutionary history. Our goal is to reconstruct gene orders in the ancestral species, while minimizing the overall number of rearrangement operations that had to ...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2014
ISSN: 1471-2105
DOI: 10.1186/s12859-014-0354-6