Hi all,
For my analysis I would like to run a plasmid phylogeny of around 400 complete plasmid from NCBI. I have saw many people use Mauve/Mugsy for alignment and further phylip /RaxML/PhyMl for generate the tree?
What's your opinion? Please share. All suggestion will be greatly appreciate.
It depends on the size of your plasmids. If they're smallish, you might be able to align them using Muscle or Mafft. Otherwise, or in the case where synteny might not be conserved across plasmids, you ought to use a genome aligner like Mauve.
Unless your plasmids are very small, your best bet to get a phylogeny that will finish in a reasonable time is RAxML, assuming you want to do some sort of model-based phylogenetics. With a dataset of this size, most Bayesian approaches will not converge quickly.
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version 2.3.6
The size and number of plasmid in between 10kb-300kb, 200 respectively. Small query: so after running Mauve I have to generate a .nexus or fasta file for input to RaxML. Could you please let me know how can I convert .xmfa (mauve out put) to .nexus?