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jjmccollum
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teiphy
A Python package for converting TEI XML collations to NEXUS, BEAST 2.7 XML, and other formats
MIT License
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:bug: Added rootFrequencies attribute (and, for convenience, value at…
#90
jjmccollum
closed
1 month ago
0
Update BEAST ancestral state/sequence logger template to reference rootFrequencies
#89
jjmccollum
closed
1 month ago
0
Use letters for states greater than 9 in STEMMA outputs
#88
jjmccollum
opened
1 month ago
0
85 add support for time dependent substitution models with epochsubstitutionmodel in beast outputs
#87
jjmccollum
closed
5 months ago
0
84 add option for choice of ancestralsequencelogger or ancestralstatelogger for beast outputs
#86
jjmccollum
closed
6 months ago
0
Add support for time-dependent substitution models with EpochSubstitutionModel in BEAST outputs
#85
jjmccollum
closed
5 months ago
2
Add option for choice of AncestralSequenceLogger or AncestralStateLogger for BEAST outputs
#84
jjmccollum
closed
6 months ago
0
82 change ancestralstatelogger to ancestralsequencelogger in beast output
#83
jjmccollum
closed
7 months ago
0
Change AncestralStateLogger to AncestralSequenceLogger in BEAST output
#82
jjmccollum
closed
7 months ago
0
:bug: Fixed beast_template.xml to include/exclude BDSKY origin distri…
#81
jjmccollum
closed
7 months ago
0
Use fixed origin for BEAST BDSKY model if tradition has a fixed composition date
#80
jjmccollum
closed
7 months ago
0
:zap: Updated tabular output options; :zap: added support for creatin…
#79
jjmccollum
closed
10 months ago
0
Change CSV outputs to include BOM
#78
jjmccollum
closed
10 months ago
1
Add support for NEXUS-style CSV/Excel output
#77
jjmccollum
closed
10 months ago
1
:zap: Added support for --seed option, changed transcriptional rate b…
#76
jjmccollum
closed
1 year ago
0
Assignment of random starting rate parameter values, new prior distributions, and support for `--seed` option
#75
jjmccollum
closed
1 year ago
0
:zap: Updated collation.to_stemma to write relative path to chron fil…
#74
jjmccollum
closed
1 year ago
0
Relative path to chron file for stemma output
#73
rbturnbull
closed
1 year ago
2
Create directory for output if needed
#72
rbturnbull
closed
10 months ago
1
Update README.rst
#71
chapnitsky
closed
1 year ago
0
Merged beast-xml branch
#70
jjmccollum
closed
1 year ago
0
add tip date sampling for beast
#69
rbturnbull
closed
1 year ago
5
Substantive units
#68
jjmccollum
closed
1 year ago
0
Listwit validation
#67
jjmccollum
closed
1 year ago
0
Add support for BEAST XML output
#66
jjmccollum
closed
1 year ago
73
Should teiphy convert all variation units, including trivial ones?
#65
jjmccollum
closed
1 year ago
0
Failure with no user-oriented error message
#64
cmsmcq
closed
1 year ago
10
Patch 1
#63
danielskatz
closed
1 year ago
1
Bump certifi from 2022.9.24 to 2022.12.7
#62
dependabot[bot]
closed
1 year ago
0
Iqtree fix
#61
rbturnbull
closed
1 year ago
0
Fix github actions workflow for iqtree
#60
rbturnbull
closed
1 year ago
1
Code revisions from second review
#59
jjmccollum
closed
1 year ago
0
Add `--long-table` option for tabular output
#58
jjmccollum
closed
1 year ago
0
Incorporate latest feedback on paper
#57
jjmccollum
closed
1 year ago
0
Add support for `--ascertainment` option
#56
jjmccollum
closed
1 year ago
4
Make `--states-present` default option for NEXUS output
#55
jjmccollum
closed
1 year ago
0
Added support for taxon date calibration with MrBayes and BEAST2 NEXUS output
#54
jjmccollum
closed
1 year ago
0
:abc: Did a pass at revising paper (#52)
#53
jjmccollum
closed
1 year ago
0
Revise paper
#52
jjmccollum
closed
1 year ago
6
Updated readme and advanced usage documentation (#50)
#51
jjmccollum
closed
1 year ago
0
Update documentation
#50
jjmccollum
closed
1 year ago
2
App --version command and PHYLIP and FASTA support
#49
jjmccollum
closed
1 year ago
0
Add support for PHYLIP and FASTA formats
#48
jjmccollum
closed
1 year ago
3
Add --version argument to app
#47
jjmccollum
closed
1 year ago
10
Exampledocs
#46
jjmccollum
closed
2 years ago
0
Example in docs
#45
rbturnbull
closed
2 years ago
2
logo/banner
#44
rbturnbull
closed
2 years ago
12
cicd
#43
jjmccollum
closed
2 years ago
0
docs for command line flags
#42
rbturnbull
closed
2 years ago
6
CHARSTATELABELS block?
#41
rbturnbull
closed
2 years ago
4
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