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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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Track PyPi URL change for project homepage
#162
mmore500
closed
3 months ago
0
Add developer documentation
#161
mmore500
closed
1 year ago
0
Some examples in `/docs/source/examples` are broken
#160
mmore500
opened
1 year ago
0
Keep supporting Python2.7?
#159
mmore500
closed
3 months ago
3
Fix broken tests, miscellaneous lint
#158
mmore500
closed
1 year ago
3
Setup CI
#157
mmore500
closed
1 year ago
3
WIP Setup CI
#156
mmore500
closed
1 year ago
1
Remove deprecated `random.sample` from `Tree.shuffle_taxa()`
#155
mmore500
closed
1 year ago
1
`shuffle_taxa` raises `DeprecationWarning`
#154
mmore500
closed
1 year ago
0
Fix unexpected rooting side effects of `Tree.mrca()`
#153
mmore500
closed
1 year ago
0
`Tree.mrca` has side effect of changing rooting state
#152
mmore500
closed
3 months ago
6
Corrected step number calculation for unrooted trees
#151
SynedraAcus
closed
1 year ago
0
API docs
#150
wsdewitt
closed
1 year ago
1
Fix minor copy/paste pre/post-order typos in docs
#149
mmore500
closed
1 year ago
0
Bugfix: Tree mrca method does not account for internal unifurcation
#148
mmore500
closed
1 year ago
2
Fixup docstring code block
#147
mmore500
closed
1 year ago
1
Underscores appear to be removed in tree taxonnamespace
#146
Mahim1997
closed
1 year ago
1
Correctly load newick node annotations containing nested lists
#145
willdumm
opened
1 year ago
0
Special characters in input tree tip labels causes unpredictable renaming
#144
AlesBucek
closed
3 months ago
6
Should `Node.extract_subtree` return Tree, not seed node, & copy annotations?
#143
MordorianGuy
opened
2 years ago
0
multiprocess :: mp.cpu_count() instead of len(os.sched_getaffinity(0))
#142
EricDeveaud
opened
2 years ago
0
Calling tab complete on a tree surpresses unifurcations in Python 3.7.3
#141
emilydolson
closed
3 months ago
1
Documentation appears to be down
#140
ericmjl
closed
2 years ago
2
Help catching exception?
#139
snacktavish
closed
2 years ago
2
Creating new tree from seed node removes node from original tree
#138
Adam-Gleave
closed
3 months ago
1
please create a release
#137
joelb123
closed
1 year ago
6
Use `case_sensitive_taxon_labels` in kwargs to set TaxonNamespace is_case_sensitive
#136
crosenth
closed
3 years ago
1
ValueError: Attempting case sensitive read with case insensitive TaxonNamespace
#135
crosenth
closed
3 years ago
1
Typo in PhylogeneticIndependentContrasts class
#134
Puumanamana
closed
3 years ago
1
Re-enable secure SSL in setup.py
#133
kislyuk
closed
3 months ago
3
raxml set rand seed
#132
NoahAmsel
closed
3 years ago
1
Can't set random seed or substitution model in RAxML wrapper
#131
NoahAmsel
closed
3 months ago
1
Dendropy web page with documentation is not working
#130
fpichardom
closed
3 years ago
1
Add label lookup to improve nexusreader speed
#129
SamStudio8
closed
3 years ago
7
added faster tree generation
#128
NicolaDM
closed
3 years ago
0
PhylogeneticDistanceMatrix.distances: return symmetric distances
#127
nick-youngblut
closed
3 months ago
4
resolve_polytomies could return number of polytomies resolved
#126
hyanwong
opened
3 years ago
0
Please tag a new release that contains 972d12fe2be3241c33fb2a969e5f0271158a24fc
#125
jonchang
closed
3 years ago
6
Add Bandelt Encoding
#124
Kuanhao-Chao
closed
4 years ago
0
Bipartition.edge
#123
jtfield
closed
4 years ago
5
Test suite vanished from download tarball
#122
tillea
opened
4 years ago
4
dendropy.utility.error.UltrametricityError
#121
nick-youngblut
opened
4 years ago
2
accuracy of gene tree simlation
#120
zzbbf123
opened
5 years ago
0
Calling the Paup tree estimate method returns an error
#119
mlalith2006
closed
11 months ago
1
Unexpected unifurcation suppression in reroot_at_node()
#118
psathyrella
closed
5 years ago
2
Best way to add a long branch above root
#117
psathyrella
closed
5 years ago
2
Fixing bug in contained_coalescent_tree function.
#116
joaks1
closed
5 years ago
1
Bug in dendropy.model.coalescent.contained_coalescent_tree
#115
joaks1
closed
5 years ago
2
phylogenetic distances with gigantic tree
#114
b-tierney
closed
5 years ago
4
TaxonNamespace partition() not working
#113
sojovictor
closed
4 years ago
4
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