Comments (1)
the variability here likely comes from random assignment of mutations to branches on either side of the root. Randomness can also arise when your tree has polytomies that are resolved by treetime and there are equal possibilities. If you send me the data, I'd be happy to have a look.
from treetime.
Related Issues (20)
- More than one record found in handle HOT 4
- how to convert the annotated nexus file (from treetime mugration) to JSON format? HOT 2
- New crash when running without alignment HOT 1
- Joint ancestral sequence reconstruction fails when input sequences are identical and GTR is inferred
- Not generating confidence intervals of divergence times, rate or root date HOT 1
- skyline: TypeError: can't multiply sequence by non-int of type 'float'
- ENH: Better error message when input alignment has sequences of unequal length HOT 1
- Newick formatting error fasttree HOT 3
- IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed HOT 2
- [read_vcf] Convert ALT '*' to "N"
- [write_vcf] CHROM is "MTB_anc"
- ERROR: Cannot read metadata: need at least one column that contains the taxon labels. HOT 7
- Different output trees HOT 2
- How to resolve Polytomies in the tree HOT 2
- BUG: clock_filter_method='residuals' should be 'residual' HOT 1
- about the mugration HOT 2
- incorrectly mutation-annotated branch on phylogeny HOT 1
- TreeTimeUnknownError: Error: Unexpected behavior detected in multiply function when determining peak of function with y-values '[]'. HOT 6
- Question about branch length in mugration
- 'branch_mutations.txt' output always empty (v 0.11.3)
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from treetime.