jeetsukumaran/DendroPy

Issues

• Reroot at edge may assign edge labels incorrectly

  #216 opened 2 months ago by terrycojones
  7

• PhylogeneticDistanceMatrix methods are awkward to use because the Taxon class uses is in its __eq__ method

  #215 opened 2 months ago by terrycojones
  1

• Multithreaded option fails with no error message - leaf labels issue?

  #180 opened 5 months ago by AthinaGav
  2

• Support values written as quoted node labels since >4.6.1

  #200 opened 7 months ago by alpae
  4

• Final Steps for Version 5 Release

  #197 opened 7 months ago by mmore500
  0

• `Tree.mrca` has side effect of changing rooting state

  #152 opened 7 months ago by mmore500
  6

• JOSS Paper?

  #198 opened 7 months ago by mmore500
  0

• Provide public interface for `_convert_node_to_root_polytomy`

  #169 opened 2 years ago by mmore500
  1

• Creating new tree from seed node removes node from original tree

  #138 opened 8 months ago by Adam-Gleave
  1

• Special characters in input tree tip labels causes unpredictable renaming

  #144 opened 8 months ago by AlesBucek
  6

• Some examples in `/docs/source/examples` are broken

  #160 opened 2 years ago by mmore500
  0

• resolve_polytomies could return number of polytomies resolved

  #126 opened 4 years ago by hyanwong
  0

• Test suite vanished from download tarball

  #122 opened 5 years ago by tillea
  4

• accuracy of gene tree simlation

  #120 opened 5 years ago by zzbbf123
  0

• Calling tab complete on a tree surpresses unifurcations in Python 3.7.3

  #141 opened 8 months ago by emilydolson
  1

• PhylogeneticDistanceMatrix.distances: return symmetric distances

  #127 opened 8 months ago by nick-youngblut
  4

• Can't set random seed or substitution model in RAxML wrapper

  #131 opened 8 months ago by NoahAmsel
  1

• Correctly load newick node annotations containing nested lists

  #145 opened 2 years ago by willdumm
  0

• Chore: Fix `ResourceWarning`s from tests

  #165 opened 2 years ago by mmore500
  0

• multiprocess :: mp.cpu_count() instead of len(os.sched_getaffinity(0))

  #142 opened 2 years ago by EricDeveaud
  0

• Should `Node.extract_subtree` return Tree, not seed node, & copy annotations?

  #143 opened 2 years ago by MordorianGuy
  0

• dendropy.utility.error.UltrametricityError

  #121 opened 5 years ago by nick-youngblut
  2

• `paup_estimate_tree_nj` example experiences intermittent failure

  #168 opened 8 months ago by mmore500
  1

• Chore: fix `distutils` deprecation warning

  #166 opened 8 months ago by mmore500
  1

• Re-enable secure SSL in setup.py

  #133 opened 8 months ago by kislyuk
  3

• Keep supporting Python2.7?

  #159 opened 8 months ago by mmore500
  3

• Track PyPi URL change for project homepage

  #162 opened 8 months ago by mmore500
  0

• Create smoke tests

  #179 opened 8 months ago by connoryang1
  0

• treesim.birth_death_tree() raises division by zero error when used to extend an existing tree

  #188 opened 8 months ago by Androstane
  4

• Error runnig picrust due to cannot import name '_convert_node_to_root_polytomy'

  #182 opened 8 months ago by Zathzk
  2

• Website dendropy.org is down

  #185 opened 8 months ago by Wytamma
  5

• Documentation Deployment

  #177 opened a year ago by mmore500
  0

• Calling the Paup tree estimate method returns an error

  #119 opened a year ago by mlalith2006
  1

• quote_underscores argument unrecognized

  #172 opened a year ago by davidrasm
  1

• please create a release

  #137 opened 2 years ago by joelb123
  6

• Add developer documentation

  #161 opened 2 years ago by mmore500
  0

• API docs

  #150 opened 2 years ago by wsdewitt
  1

• `shuffle_taxa` raises `DeprecationWarning`

  #154 opened 2 years ago by mmore500
  0

• Underscores appear to be removed in tree taxonnamespace

  #146 opened 2 years ago by Mahim1997
  1

• Documentation appears to be down

  #140 opened 3 years ago by ericmjl
  2

• Help catching exception?

  #139 opened 3 years ago by snacktavish
  2

• ValueError: Attempting case sensitive read with case insensitive TaxonNamespace

  #135 opened 4 years ago by crosenth
  1

• Typo in PhylogeneticIndependentContrasts class

  #134 opened 4 years ago by Puumanamana
  1

• Dendropy web page with documentation is not working

  #130 opened 4 years ago by fpichardom
  1

• Please tag a new release that contains 972d12fe2be3241c33fb2a969e5f0271158a24fc

  #125 opened 4 years ago by jonchang
  6

• Bipartition.edge

  #123 opened 5 years ago by jtfield
  5

• Unexpected unifurcation suppression in reroot_at_node()

  #118 opened 5 years ago by psathyrella
  2

• Best way to add a long branch above root

  #117 opened 6 years ago by psathyrella
  2

• Bug in dendropy.model.coalescent.contained_coalescent_tree

  #115 opened 6 years ago by joaks1
  2

• phylogenetic distances with gigantic tree

  #114 opened 6 years ago by b-tierney
  4