منابع مشابه
SequenceLDhot: detecting recombination hotspots
MOTIVATION There is much local variation in recombination rates across the human genome--with the majority of recombination occurring in recombination hotspots--short regions of around approximately 2 kb in length that have much higher recombination rates than neighbouring regions. Knowledge of this local variation is important, e.g. in the design and analysis of association studies for disease...
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Despite the small amount of genetic variation segregating amongst our House Finch Mycoplasma samples (only 412 SNPs), it is not possible to build a single phylogenetic tree with no homoplasies from this data. Similarly, although our poultry strains contained many more SNPs between them, one still cannot infer a single phylogenetic tree that has much more support than alternate trees. The reason...
متن کاملDetecting Sporadic Recombination in DNA Alignments with Hidden Markov Models
Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the...
متن کاملDetecting interspecific recombination with a pruned probabilistic divergence measure
MOTIVATION A promising sliding-window method for the detection of interspecific recombination in DNA sequence alignments is based on the monitoring of changes in the posterior distribution of tree topologies with a probabilistic divergence measure. However, as the number of taxa in the alignment increases or the sliding-window size decreases, the posterior distribution becomes increasingly diff...
متن کاملProbabilistic divergence measures for detecting interspecies recombination
This paper proposes a graphical method for detecting interspecies recombination in multiple alignments of DNA sequences. A fixed-size window is moved along a given DNA sequence alignment. For every position, the marginal posterior probability over tree topologies is determined by means of a Markov chain Monte Carlo simulation. Two probabilistic divergence measures are plotted along the alignmen...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2002
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/18.suppl_1.s345