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

207 stars 62 forks source link

issues

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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
Preserve_underscores

#112 wrightaprilm opened 5 years ago
2
Use dictionary.items instead of iteritems for Python3 Compatibility

#111 petercombs closed 5 years ago
1
Seg Fault when deepcopy-ing large tree

#110 MGNute closed 1 year ago
4
Bipartition comparison depends on rootedness

#109 benjaminwilson closed 5 years ago
5
RNG seed doesn't determine result of `treesim.birth_death_tree`

#108 benjaminwilson closed 5 years ago
4
NewickReaderMalformedStatementError: NewickReaderMalformedStatementError

#107 snowflake01986 closed 1 year ago
1
Typo in treemeasure.py

#106 ArtPoon closed 5 years ago
1
Missing space in DIMENSIONS command when writing DataSet to simple NEXUS format

#105 jmenglund closed 5 years ago
1
fix typos in primer/treemanips.rst

#104 wosnat closed 5 years ago
1
single / to double //, with a single slash url is interpreted as rel…

#103 Carreau closed 5 years ago
1
suppress_unifurcations=False when computing bipartitions after unrooting is broken

#102 thekswenson closed 5 years ago
3
keep_sequences() issue

#101 wrightaprilm closed 6 years ago
4
Bipartition is mutable: hash is unstable

#100 any333 closed 6 years ago
3
MRCA algorithm can be faster

#99 niemasd opened 6 years ago
1
as_ascii_plot() kwargs not showing up in docs

#98 psathyrella closed 6 years ago
1
documentation: viewing and displaying Newick tree needs semi-colon

#97 thekswenson closed 6 years ago
1
Tests not included in pypi release

#96 wwood closed 6 years ago
6
extract_tree_with_taxa + str() produces malformed tree

#95 niemasd closed 5 months ago
5
Update index.rst

#94 wrightaprilm closed 6 years ago
6
popgenstat behavior is strange

#93 tiagoantao closed 6 years ago
3
GenBank generate_char_matrix requires a pre-loaded TaxonNamespace

#92 tiagoantao closed 6 years ago
5
Documentation for GenBank generate_char_matrix inconsistent with code

#91 tiagoantao closed 6 years ago
2
Install version available at a specific date

#90 madzafv closed 6 years ago
2
`split_distribution` crashes with `TypeError`

#89 mjr129 closed 5 months ago
2
random seed reproducibility of treesim.birth_death_tree when using numpy.save

#88 idavydov closed 5 months ago
1
Error in CharacterDataSequence.annotations_at when loading Phenoscape Ontotrace NeXML file

#87 gaurav closed 6 years ago
2
functions extract_tree_with_taxa and extract_tree_with_taxa_labels have extra parameters in the documentation

#86 idavydov closed 5 months ago
1
Maximum recursion depth

#85 MrOlm closed 7 years ago
1
default standard alphabet is 01 not 0123456789 as per docs

#84 rhr closed 7 years ago
1
Is there a summarization demo of the DendroPy/

#83 JafferWilson closed 5 months ago
1
DNACharacterMatrix.export_character_indices() very slow

#82 brunoasm closed 7 years ago
7
Dedropy mistakenly looking for DNA alphabet in ProteinCharacterMatrix.get

#81 tauanajc closed 5 months ago
2
as_python_source is not working

#80 idavydov closed 7 years ago
1
as_newick_string() changed to _as_newick_string()

#79 josephryan closed 7 years ago
3
Documentation formatting

#78 beroe closed 7 years ago
4
test failures: unorderable types: Edge() < Edge()

#77 rekado closed 7 years ago
1
Dendropy incorrectly reads terminating unnamed unifurcations

#76 hyanwong closed 5 months ago
3
Feature request: suppress_unifurcations() to return number of unifurcations suppressed

#75 hyanwong closed 7 years ago
3
test failure on ubuntu with python 2.7.11+

#74 mtholder closed 1 year ago
1
Error installing DendroPy along Python 2.7 on Mac OS

#73 RubenRBakker closed 7 years ago
3
resolve_polytomies inconsistently creates 0-length branches

#72 hyanwong closed 7 years ago
2
sumlabels?

#71 courtneystairs closed 7 years ago
4
uncaught exception when using "plot_metric='length'" without lengths

#70 daveuu closed 8 years ago
2
rerooting trifurcated tree issue

#69 geronimp closed 8 years ago
2
Duplicating trees while pruning

#68 wrightaprilm closed 8 years ago
4
Typo fix

#67 snacktavish closed 8 years ago
2

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