When do we normally look at recombination in a large dataset of bacterial genomes- is this particularly important for medical pathogen? How do we normally interpret this?
Dear Raymond,
I recommend you to perform first your analysis with Mauve:
MAUVE is Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.
http://darlinglab.org/mauve/mauve.html
After is possible to analysis the specifics genes for recombination with:
- http://ve.oxfordjournals.org/content/vevolu/1/1/vev003.full.pdf; or
- http://www.datamonkey.org/
You may refer to the following publication:
http://nar.oxfordjournals.org/content/43/14/6761.long
Recombination can really distort branch lengths in bacterial phylogenies. Use algorithms like Gubbins and ClonalFrameML to detect regions of elevated snp density and generate final phylogenetic trees free of recombination.
https://github.com/sanger-pathogens/gubbins
https://github.com/xavierdidelot/ClonalFrameML
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