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neherlab
/
treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
MIT License
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Make fasta reader alphabet-aware (error version)
#283
ivan-aksamentov
closed
3 weeks ago
0
Make fasta reader alphabet-aware (filter version)
#282
ivan-aksamentov
closed
3 weeks ago
0
refactor: inline get_clock_model()
#281
ivan-aksamentov
closed
1 month ago
0
refactor: clock regression steps
#280
ivan-aksamentov
closed
1 month ago
0
refactor: ClockOptions construction
#279
ivan-aksamentov
closed
1 month ago
0
Refactor/clock
#278
rneher
closed
1 month ago
0
Fix/ancestral tests
#277
rneher
closed
1 month ago
0
Fix/ancestral tests
#276
rneher
closed
1 month ago
0
Documentation on CLI function 'clock' is wrong. Date has to be date format not year decimal.
#275
m-d-grunnill
opened
2 months ago
1
MissingDataError: ERROR: Cannot read metadata:
#274
aliciapm7
opened
4 months ago
3
fix: fix nwk writer
#273
rneher
closed
4 months ago
0
'branch_mutations.txt' output always empty (v 0.11.3)
#272
LewisCEMason
closed
1 month ago
2
Question about branch length in mugration
#271
Tonny-zhou
opened
6 months ago
1
TreeTimeUnknownError: Error: Unexpected behavior detected in multiply function when determining peak of function with y-values '[]'.
#270
bacterpang
closed
1 month ago
7
incorrectly mutation-annotated branch on phylogeny
#269
akifoss
opened
7 months ago
1
about the mugration
#268
bacterpang
closed
6 months ago
2
BUG: clock_filter_method='residuals' should be 'residual'
#267
zacmon
closed
7 months ago
1
How to resolve Polytomies in the tree
#266
Sikandar37
closed
7 months ago
2
Different output trees
#265
MarliesJFrancine
closed
7 months ago
2
ERROR: Cannot read metadata: need at least one column that contains the taxon labels.
#264
timeresistance1996
closed
7 months ago
7
Improve VCF parsing
#263
jameshadfield
closed
8 months ago
5
[write_vcf] CHROM is "MTB_anc"
#262
jameshadfield
closed
8 months ago
0
[read_vcf] Convert ALT '*' to "N"
#261
jameshadfield
closed
8 months ago
0
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
#260
ritawyt
opened
11 months ago
2
Newick formatting error fasttree
#259
hbarbian
closed
11 months ago
3
ENH: Better error message when input alignment has sequences of unequal length
#258
corneliusroemer
opened
1 year ago
1
docs: Improve docstring of parse_dates
#257
corneliusroemer
closed
1 year ago
0
skyline: TypeError: can't multiply sequence by non-int of type 'float'
#256
judyssister
opened
1 year ago
0
fix: regularize mutation rate calculation
#255
rneher
closed
1 year ago
0
Not generating confidence intervals of divergence times, rate or root date
#254
katie110621
opened
1 year ago
1
Joint ancestral sequence reconstruction fails when input sequences are identical and GTR is inferred
#253
huddlej
closed
1 year ago
0
Address Pytest warning
#252
corneliusroemer
closed
1 year ago
0
Fix: Only write auspice.json when there is sequence information
#251
corneliusroemer
closed
1 year ago
0
New crash when running without alignment
#250
theosanderson
closed
1 year ago
1
how to convert the annotated nexus file (from treetime mugration) to JSON format?
#249
judyssister
closed
1 year ago
2
Feat/outlier detection
#248
rneher
closed
1 year ago
0
More than one record found in handle
#247
ashotmarg
opened
1 year ago
4
A value in x_new is above the interpolation range's maximum value
#246
michaeljon
closed
1 year ago
2
Binary Sequence Alignement
#245
adrienlemeur
opened
1 year ago
3
Fix/probability loss2
#244
rneher
closed
1 year ago
0
Fix/probability loss
#243
rneher
closed
1 year ago
0
`IndexError: index 0 is out of bounds for axis 0 with size 0` in `--use-fft` mode
#242
corneliusroemer
closed
1 year ago
3
ENH: Allow /dev/stdin as input alignment arg
#241
corneliusroemer
opened
1 year ago
0
The new stochastic_resolve function didn't properly check
#240
rneher
closed
1 year ago
1
Unexpected behavior detected in multiply function when determining peak of function with y-values
#239
josephhughes
closed
1 year ago
17
Add Python 3.11 tests to ci.yml
#238
corneliusroemer
closed
1 year ago
0
Add `python_requires>=3.7` to setup.py
#237
corneliusroemer
opened
1 year ago
0
Update RNG changelog entry
#236
victorlin
closed
1 year ago
0
more strict condition for fall back on delta function convolution
#235
rneher
closed
1 year ago
0
Fix/export and polytomies
#234
rneher
closed
1 year ago
0
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