Comments (1)
This is a poorly documented requirement, but you need to either supply treetime with a standard deviation of your clock estimate (add something like --clock-std-dev 0.0003
to the command) , or run it with --covariation
.
from treetime.
Related Issues (20)
- ERROR: No variation in sampling dates! Please specify your clock rate explicitly HOT 7
- ENH: Make multiple root-to-tip-plots to help with debugging
- Typo in documentation HOT 1
- ERROR: local variable 'peak' referenced before assignment HOT 4
- Unexpected behavior detected in multiply function when determining peak of function with y-values HOT 17
- ENH: Allow /dev/stdin as input alignment arg
- `IndexError: index 0 is out of bounds for axis 0 with size 0` in `--use-fft` mode HOT 3
- Binary Sequence Alignement HOT 3
- A value in x_new is above the interpolation range's maximum value HOT 2
- 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
- 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"
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from treetime.