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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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what are the best parameters that can be use for identical sequences in Raxml? #373

Closed SachiiM closed 1 year ago

SachiiM commented 1 year ago

I have a set of 22 sequences that are identical, except for one sequences which differ in 2 bp compared to the rest. Although the sequences are identical I still require to generate a ML tree for these sequences.

I ran the RXML tree with Rapid bootstrap GTR GAMMA to generate a tree. However instead of obtaining polytomy, I'm observing a clade separation for the identical sequences which is not accurate. Can someone help me how to deal with this?

Thank you

nickjcroucher commented 1 year ago

This is not a Gubbins-related issue.