I am trying to run TimeTree on a bacterial dataset. I successfully run it with a relaxed clock model (--relax 1.0 0.5), but I end up with 2 polytomies, each consisting of 3 isolates, in my final tree (timetree.pdf file).
Why would polytomies appear in the final tree? Could this be a sign of something not being right in the analysis/with the input data? The data is moderately clock-like (r^2 = ~0.57), but I figured this would be okay for a relaxed clock approach...the polytomies in question have a minimum distance of 2 SNPs between the closest 2 isolates, and 4-6 SNPs between the most distant two, so no two isolates are identical and under a standard ML phylogenetic approach, no polytomies are formed...
I have also tried running it without the "--relax" option (strict clock?) and the polytomes remain.
Any help in understanding why this might be occurring would be greatly appreciated.
cizydorczyk
commented
5 years ago
Hello,
I am trying to run TimeTree on a bacterial dataset. I successfully run it with a relaxed clock model (--relax 1.0 0.5), but I end up with 2 polytomies, each consisting of 3 isolates, in my final tree (timetree.pdf file).
Why would polytomies appear in the final tree? Could this be a sign of something not being right in the analysis/with the input data? The data is moderately clock-like (r^2 = ~0.57), but I figured this would be okay for a relaxed clock approach...the polytomies in question have a minimum distance of 2 SNPs between the closest 2 isolates, and 4-6 SNPs between the most distant two, so no two isolates are identical and under a standard ML phylogenetic approach, no polytomies are formed...
I have also tried running it without the "--relax" option (strict clock?) and the polytomes remain.
Any help in understanding why this might be occurring would be greatly appreciated.
Thank you, Conrad Izydorczyk