Comments (1)
In some modes, TreeTime collapses branches that are not supported. But the output should generally have either 6 or 8 digits precision, depending on the length of the genome being used. In the mugration step, there is typically no genome and this might be restrict the precision to 6 digits. I have increased precision a bit. Hopefully this fixes your problem.
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Related Issues (20)
- 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 7
- 'branch_mutations.txt' output always empty (v 0.11.3) HOT 2
- MissingDataError: ERROR: Cannot read metadata: HOT 2
- Documentation on CLI function 'clock' is wrong. Date has to be date format not year decimal. HOT 1
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