Comments (1)
The example scripts were moved into a separate repository:
https://github.com/neherlab/treetime_examples/tree/master/scripts
Furthermore, we exposed this functionality as a command line tool, see here for a usage example:
https://github.com/neherlab/treetime_examples/blob/master/ancestral.md
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Related Issues (20)
- 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 7
- Question about branch length in mugration HOT 1
- 'branch_mutations.txt' output always empty (v 0.11.3) HOT 2
- MissingDataError: ERROR: Cannot read metadata: HOT 2
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