matsengrp/gctree

Issues

• ValueError: Zero likelihood event

  #105 opened 3 months ago by chaoszhang
  7

• Incorrect dnapars outfile parsing

  #113 opened 3 months ago by willdumm
  0

• Qt platform plugin could be initialized

  #127 opened 5 months ago by NSchwanPhy
  2

• Extreme Runtime

  #124 opened 6 months ago by lejecrs
  5

• Tree visualization without the number text

  #119 opened 7 months ago by markutz556
  2

• Phylip Installaion

  #123 opened 7 months ago by vivekruhela
  4

• update historydag version requirement

  #121 opened 8 months ago by jgallowa07
  1

• Disagreement in node coloring for (some) identical sequences

  #120 opened 9 months ago by victor-ramos
  6

• Tree inference taking very long time - advice needed

  #117 opened 10 months ago by fabio-t
  11

• Rethink isotype inference

  #116 opened a year ago by willdumm
  0

• Support for Python 3.10

  #82 opened a year ago by willdumm
  0

• GitHub action runner OS not set

  #114 opened a year ago by wsdewitt
  0

• Rename master branch to main

  #98 opened 2 years ago by matsen
  0

• swap master --> main

  #111 opened 2 years ago by psathyrella
  1

• Allow all ranking stats to be computed on individual `CollapsedTree`s

  #109 opened 2 years ago by willdumm
  1

• Add option to recover all top-ranked trees instead of sampling from topology classes

  #107 opened 2 years ago by willdumm
  0

• gctree infer with --tree-stats argument does not write pickled tree outputs

  #106 opened 2 years ago by willdumm
  1

• to support amino acids sequences

  #108 opened 2 years ago by cjhong
  1

• interface with SAMM or bypass Galton branching

  #104 opened 2 years ago by Lan-h
  7

• Jumble parameter for tree space search should be user configurable

  #101 opened 2 years ago by wsdewitt
  6

• Ability to count reversions

  #90 opened 2 years ago by matsen
  1

• local branching metric harmonization

  #99 opened 2 years ago by wsdewitt
  0

• accommodate ambiguous observed sequences

  #71 opened 2 years ago by willdumm
  7

• `import gctree` causes `FloatingPointError` in independent matplotlib/numpy calls

  #92 opened 2 years ago by wsdewitt
  2

• Errors installing PyQt5 dependency on ARM Mac using pip

  #95 opened 2 years ago by wsdewitt
  0

• stringified tuple sequence name

  #87 opened 2 years ago by psathyrella
  0

• Various comments/suggestions

  #84 opened 2 years ago by psathyrella
  3

• find identical mamaras in the tree

  #53 opened 3 years ago by matsen
  10

• Problem with Sequence IDs

  #58 opened 3 years ago by fabio-t
  10

• Default help menu missing

  #59 opened 3 years ago by fabio-t
  1

• restrict tuple-valued node names to bootstrap trees

  #64 opened 3 years ago by wsdewitt
  0

• Consistent Numpy underflow error on some machines

  #67 opened 3 years ago by willdumm
  2

• obey isotype switching order

  #63 opened 3 years ago by willdumm
  4

• Any parallel or accelerated parameters?

  #66 opened 3 years ago by liyi522
  1

• Error: scons: *** No SConstruct file found.

  #45 opened 4 years ago by jonoave
  3

• Phylip_parse.disambiguate sometimes chooses non-optimal tree

  #56 opened 3 years ago by willdumm
  0

• It is possible parallel processing in step python -u bin/gctree.py

  #42 opened 3 years ago by Chuang1118
  5

• Plot are not generated due to a problem with Qt

  #49 opened 3 years ago by Aurelien-Pelissier
  3

• update README (and potentially web link) with reference for full paper

  #52 opened 3 years ago by matsen
  1

• Error: Biopython

  #46 opened 3 years ago by jonoave
  1

• Dockerfile, and a release

  #37 opened 3 years ago by matsen
  0

• colors in hex

  #47 opened 3 years ago by cstrlln
  2

• Data inconsistency between simulation and inference

  #44 opened 4 years ago by NikaAb
  3

• About the output file when using the --bootstrap option

  #43 opened 4 years ago by xvtyzn
  2

• --idlabel not working?

  #41 opened 5 years ago by cstrlln
  2

• use of color argument

  #40 opened 5 years ago by cstrlln
  3

• Limit of abundance for each sequence

  #39 opened 5 years ago by NikaAb
  5

• Fasta file with variable sequence length

  #38 opened 5 years ago by NikaAb
  2

• Output the best tree as newick

  #35 opened 6 years ago by krdav
  0

• Installation or user idiocy problem

  #36 opened 7 years ago by vnminin
  6