How to calculate the number of singleton in phylogenetic network?

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Yanjing Wang

Hi Giang,

Do you mean the singleton haplotyps? Singleton haplotypes are haplotypes that were only one in your samples.

Brian Thomas Foley

I don't know anything about Fluxus or your "network", but our "elimdupes" program counts the number of occurrences of identical sequences in a multiple sequence alignment.

https://www.hiv.lanl.gov/content/sequence/ELIMDUPES/elimdupes.html

And the output is all of the less than identical sequences plus the count added to the name of any sequence that was found in duplicate (or more). You can also set the threashold for "identity" to be 99% or any other value instead of 100% if you want to look at "families" of similar sequences rather than just 100% identical duplicates.

I am not certain this tool will work for you but it is "point and click" simple to try it and see.