jeetsukumaran DendroPy issues

jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

https://pypi.org/project/DendroPy/.

BSD 3-Clause "New" or "Revised" License

210 stars 61 forks source link

issues

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UPGMA Trees are None-rooted

#66 yasuiniko closed 8 years ago
6
faster pruning

#65 kyungtaekLIM closed 8 years ago
1
Need informations

#64 ghost closed 7 years ago
1
Floating point error accumulation in contained coalescent trees

#63 yasuiniko opened 8 years ago
0
Deep copy annotation

#62 biologyguy closed 8 years ago
1
[User Error] Bug: Error using TreeList and contained coalescent tree

#61 yasuiniko closed 8 years ago
2
Inconsistent distances from leaves to root in birth/death trees

#60 yasuiniko closed 8 years ago
8
Possible bugs setting parent_node, not _parent_node

#59 hyanwong closed 8 years ago
3
Update treecompare.py

#58 eascarrunz closed 8 years ago
4
Documentation for newick output possibly wrong

#57 hyanwong closed 6 months ago
2
Fixed issues with missing or uncertain bases in TajD calculation

#56 andrewguy closed 8 years ago
3
Optimise popgenstat._count_differences()

#55 andrewguy closed 8 years ago
3
possible enhancement: retain edge identity when rerooting

#54 mtholder opened 8 years ago
1
can node labels be parsed as support values for tree rooting purposes?

#53 jhcepas closed 8 years ago
25
Maximum recursion depth error

#52 ericmjl opened 8 years ago
8
mrca changes underlying tree?

#51 wwood closed 8 years ago
8
Probelms with DendroPy compiled with other software.

#50 Lily-WL closed 8 years ago
15
jplace style edge numbering

#49 wwood closed 8 years ago
4
python3 test failure

#48 wwood closed 8 years ago
4
sumtrees.py outputs an extra tree when onto a target tree

#47 mossmatters closed 8 years ago
1
Feature request: Writing to JSON schema

#46 Zsailer opened 8 years ago
14
PatristicDistanceMatrix

#45 basic99 closed 8 years ago
2
Add support for PhyML interoperability

#44 jmenglund closed 4 years ago
2
Avoid ZeroDivisionError comparing non-overlapping sequences

#43 hdetering closed 8 years ago
1
char. matrix `from_dict` and unicode keys

#42 mtholder closed 8 years ago
1
factories set to None can be a signal to exclude trees or chars

#41 mtholder closed 8 years ago
0
Add support for interleaved PHYLIP writing

#40 pranjalv123 closed 4 years ago
1
When reading NEXUS tree created by MrBayes, converts dashes/hyphens "-" into " " or "_"

#39 J-Moravec closed 8 years ago
8
Several bugfixes in charmatrixmodel and nexusprocessing.

#38 allista closed 8 years ago
1
Parsing NEXUS trees with undefined taxon labels does not raise error

#37 jeetsukumaran opened 9 years ago
0
Infinite loop in treemodel.Tree.reroot_at_midpoint()

#36 biologyguy closed 9 years ago
1
Inconsistent AttributeError on deepcopy

#35 biologyguy closed 9 years ago
5
Misleading sumtrees.py --usage-examples

#34 kloetzl closed 9 years ago
2
Make PHYLIP writing work correctly with missing taxa

#33 pranjalv123 closed 9 years ago
1
Common Ancestors age strategy for --set-edges

#32 nitishnarula opened 9 years ago
0
'Tree' object has no attribute 'bipartitions'

#31 donovan-h-parks closed 9 years ago
1
reroot_at_edge() causes trifurcation and incorrect branch lengths

#30 donovan-h-parks closed 9 years ago
4
PHYLIP reader can only read one character matrix per file

#29 pranjalv123 closed 9 years ago
3
leafset_taxa() missing "index" kwarg

#28 daveuu closed 9 years ago
3
bipartition.is_trivial is True for non-trivial bipartitions in v4.0.3

#27 daveuu closed 9 years ago
2
NameError raised by dendropy.calculate.treecompare.find_missing_bipartitions

#26 daveuu closed 9 years ago
2
Ordered Parsimony

#25 mccannj9 opened 9 years ago
1
Change of consensus frequency in sumtrees.py does not work

#24 tiagoantao closed 9 years ago
1
scm is not supported in Dendropy 4.0.2

#23 Kajori closed 6 months ago
2
bug in export of new characters from a char mat: need to delete or update char sets

#22 mtholder closed 9 years ago
1
Charset export

#21 mtholder closed 9 years ago
1
Fix bug where encoding for default locale is None.

#20 pranjalv123 closed 9 years ago
1
Sometimes locale.getdefaultlocale() returns (None, None)

#19 pranjalv123 closed 9 years ago
0
Is there a recommended way to run the tests in parallel?

#18 mtholder closed 1 year ago
5
Suppressing missing site-packages info for venv

#17 mtholder closed 9 years ago
2

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