Issues

• Ambiguous characters in pml

  KlausVigo/phangorn#189 · Filter by author ekopania opened on Mar 18, 2026
  4

• bootstrap.pmlPart

  KlausVigo/phangorn#186 · Filter by author cbird808 opened on Apr 29, 2025

• Why does rSPR generate multifurcating trees sometimes?

  bug
  KlausVigo/phangorn#181 · Filter by author teng-gao opened on Dec 9, 2024
  1

  

• ancestral.pml gives NaN values

  KlausVigo/phangorn#176 · Filter by author kbhoehn opened on Oct 8, 2024
  6

• Inquiry About Setting Character Weights in optim.parsimony Function

  KlausVigo/phangorn#172 · Filter by author Xinru99 opened on Aug 30, 2024
  2

• Simulate coding nucleotide sequences

  KlausVigo/phangorn#167 · Filter by author trilisser opened on Jun 6, 2024

• fix labels land plot margins in plot.networx

  KlausVigo/phangorn#166 · Filter by author KlausVigo opened on Jun 3, 2024
  

• ancestral.pars differences between 2.11.1 and 3.0.0

  KlausVigo/phangorn#165 · Filter by author colejensen opened on May 22, 2024

• Error message 'R session aborted' when running modelTest(primates)

  KlausVigo/phangorn#157 · Filter by author Zhangvvv opened on Dec 15, 2023
  2

• Data availability

  KlausVigo/phangorn#148 · Filter by author Neclow opened on May 17, 2023

• pml() segfault: memory not mapped

  KlausVigo/phangorn#144 · Filter by author iferres opened on Jan 18, 2023
  2

• How can I access the probabilities using ancestral pml of entire sequence

  KlausVigo/phangorn#132 · Filter by author xbonner13 opened on Oct 12, 2022

• Ancestral Sequence Reconstruction with ancestral.pml

  KlausVigo/phangorn#131 · Filter by author MarStreicher opened on Sep 7, 2022
  3

• Assigning different Q matrices to different morphological characters

  KlausVigo/phangorn#106 · Filter by author JMoysiuk opened on Jan 6, 2021

• Phangorn with binary state data generates error with modelTest and warning with optim.pml

  KlausVigo/phangorn#98 · Filter by author fpbarthel opened on Jun 11, 2020

• optim.pml()

  KlausVigo/phangorn#89 · Filter by author JacobAFW opened on Oct 18, 2019

• unexpected tiplabels behavior using network imported from splitstree

  KlausVigo/phangorn#88 · Filter by author tim-oconnor opened on Oct 16, 2019
  1

• One tree has a different number of tips - bootstrap.pml() function runs

  KlausVigo/phangorn#87 · Filter by author alptaciroglu opened on Oct 6, 2019
  2

• Memory not mapped error when working on DECIPHER and phangorn packages

  KlausVigo/phangorn#78 · Filter by author alptaciroglu opened on Jun 20, 2019
  2

• optim.pml not stopping iterating

  KlausVigo/phangorn#74 · Filter by author nemartins opened on May 16, 2019
  1

• optim.pml error

  KlausVigo/phangorn#69 · Filter by author Neutrino1234 opened on Mar 24, 2019
  2

• Block bootstrap for SH-test (etc)

  KlausVigo/phangorn#53 · Filter by author seb-mueller opened on Jun 12, 2018

• check df for codon models

  KlausVigo/phangorn#52 · Filter by author KlausVigo opened on May 8, 2018
  

• Using different optimization method using optim.pml

  KlausVigo/phangorn#45 · Filter by author halabikeren opened on Apr 24, 2018
  1

• 'optim.pml' error - missing value

  KlausVigo/phangorn#35 · Filter by author Saetha opened on Oct 19, 2017
  4