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add phylogeny output #7
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@gokeson this one is for you! |
#Put all of your reference sequences in a folder (all have to be fasta)
#find the ideal length of k-mer that will be used for the alignment:
#run ksnp #After kSNP4, fix the tree using ClonalFrameML to mask recombinant regions: #Use the output of k-SNP4 as the input to ClonalFrameML:
#The output files are listed here: https://github.com/xavierdidelot/clonalframeml/wiki but what we care about is the tree (.newick). Look at the (em.txt) file if you want to know the rho/theta values, branch lengths (based on recombination distance) etc. #Visualization: |
I think we should avoid computational heavy like ClonalFrameML, how long does it take to run? |
220 minutes for 125 samples to run clonalframeML after already running ksnp for 3 hours for same samples. This is where gubins may be advantageous. it requires a ref genome but Ithink that is okay. Everyone uses strain D for gubbins so why not |
And gubbins is really fast. |
#How to run gubbins my way:
#Where input.list is a tab-delimited file with one row per isolate. The first column should be the isolate name, and the subsequent entries on the same row should contain the corresponding sequence data
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On your 125 sample tree with clonalframeML, can you extract the snps which are flagged as recombinant? |
Nope. I tried but can't. |
Create phylogeny for each sample.
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