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jeetsukumaran
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DendroPy
A Python library for phylogenetic scripting, simulation, data processing and manipulation.
https://pypi.org/project/DendroPy/.
BSD 3-Clause "New" or "Revised" License
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Reroot at edge may assign edge labels incorrectly
#216
terrycojones
opened
3 weeks ago
7
PhylogeneticDistanceMatrix methods are awkward to use because the Taxon class uses is in its __eq__ method
#215
terrycojones
opened
1 month ago
1
Update citing info
#214
mmore500
closed
2 months ago
1
Incorporate feedback from JOSS Editor in Charge
#213
mmore500
closed
2 months ago
0
Further fix up JOSS ISSNs
#212
mmore500
closed
2 months ago
0
Fix ISSNs in JOSS bib
#211
mmore500
closed
2 months ago
0
Incorporate JOSS editor suggestions
#210
mmore500
closed
2 months ago
0
Update JOSS draft
#209
mmore500
closed
3 months ago
0
Touchup RE JOSS review
#208
mmore500
closed
3 months ago
1
Standardize License to BST 3 Clause
#207
mmore500
closed
3 months ago
1
Only deploy docs from main branch
#206
mmore500
closed
3 months ago
0
Improved docstring for src/dendropy/datamodel/treemodel/_tree.py/reroot_at_edge
#205
terrycojones
closed
3 months ago
2
Remove preserve_underscores as an argument in docstring example usages of datamodel.basemodel.Serializable.write
#204
terrycojones
closed
3 months ago
3
Bump certifi from 2023.7.22 to 2024.7.4 in /docs
#203
dependabot[bot]
closed
4 months ago
1
Bump urllib3 from 2.0.7 to 2.2.2 in /docs
#202
dependabot[bot]
closed
5 months ago
1
Fix unnecessary quoting in newick format
#201
mmore500
closed
5 months ago
1
Support values written as quoted node labels since >4.6.1
#200
alpae
closed
5 months ago
4
Bump requests from 2.31.0 to 2.32.0 in /docs
#199
dependabot[bot]
closed
6 months ago
1
JOSS Paper?
#198
mmore500
closed
6 months ago
0
Final Steps for Version 5 Release
#197
mmore500
closed
5 months ago
0
JOSS
#196
mmore500
closed
3 months ago
1
Fix readthedocs build
#195
mmore500
closed
6 months ago
2
Implement, test polytomize_root
#194
mmore500
opened
6 months ago
1
Warn on implicit splice operations
#193
mmore500
closed
6 months ago
0
Fix escaping of newick strings
#192
mmore500
closed
6 months ago
0
Fix newick parser handling of terminating unnamed unifurcations
#191
mmore500
closed
6 months ago
0
Fix extant/extinct bug for custom tree birthdeath
#190
mmore500
closed
6 months ago
0
Update setup.py
#189
mmore500
closed
6 months ago
0
treesim.birth_death_tree() raises division by zero error when used to extend an existing tree
#188
Androstane
closed
6 months ago
4
Bump jinja2 from 3.1.3 to 3.1.4 in /docs
#187
dependabot[bot]
closed
6 months ago
0
Option to give leaf nodes in polytomies a default order in Tree.ladderize.
#186
davipatti
closed
3 months ago
5
Website dendropy.org is down
#185
Wytamma
closed
6 months ago
5
Add codecov token
#184
mmore500
closed
6 months ago
1
Bump idna from 3.4 to 3.7 in /docs
#183
dependabot[bot]
closed
7 months ago
0
Error runnig picrust due to cannot import name '_convert_node_to_root_polytomy'
#182
Zathzk
closed
6 months ago
2
Bump jinja2 from 3.1.2 to 3.1.3 in /docs
#181
dependabot[bot]
closed
9 months ago
0
Multithreaded option fails with no error message - leaf labels issue?
#180
AthinaGav
closed
4 months ago
2
Create smoke tests
#179
connoryang1
closed
6 months ago
0
Setup deploy CI job
#178
mmore500
closed
1 year ago
1
Documentation Deployment
#177
mmore500
closed
11 months ago
0
Prepare version 5.0 release
#176
mmore500
closed
6 months ago
2
Flesh out ongoing development documentation
#175
mmore500
closed
1 year ago
1
Pin ruff linter version
#174
mmore500
closed
1 year ago
0
Switch classmethod, staticmethod to decorator syntax
#173
mmore500
closed
1 year ago
1
quote_underscores argument unrecognized
#172
davidrasm
closed
1 year ago
1
Test packaging
#171
mmore500
closed
1 year ago
1
Pass rng in evolve_states
#170
actapia
closed
1 year ago
4
Provide public interface for `_convert_node_to_root_polytomy`
#169
mmore500
opened
1 year ago
1
`paup_estimate_tree_nj` example experiences intermittent failure
#168
mmore500
closed
6 months ago
1
Fix invalid escape sequences
#167
mmore500
closed
1 year ago
3
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