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  • Tools for Detecting Recombination in Closely Related Sequences

    Hi all,

    I am working with some fungal mtDNAs and am hoping to detect evidence of recombination.

    My main issue is that these sequences (~100) are all within a species and the coding sequences have very low diversity (the non-coding regions are large and too diverse to align easily).

    The phylogenetic relationships have proven difficult to disentangle (low bootstrap values, different genes give different topologies, etc.) so it looks like recombination has obscured the relationships hugely. This would be consistent with the patterns observed in the nuclear phylogeny. I am hoping to use STRUCTURE to confirm this pattern.

    I have been looking into RDP4, as a great paper came out last year comparing some of these sequences to other yeast species and detected inter-clade recombination events.

    Unfortunately, the RDP4 manual suggests sequences not be too similar. I can detect recombination events with RDP4 in this sample but I feel like I am missing a lot of them.

    I read here that SimPlot is good but from the website it looks like it hasn't been updated since 2003 and I would prefer to use a more recent tool.

    Does anyone have any suggestions?

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