neherlab/pan-genome-analysis

Issues

• SF12_create_panGenome import ete_tree_split

  #62 opened 6 months ago by delavegapab
  0

• [Errno 2] No such file or directory: -> tmp_core_diversity.txt

  #58 opened 2 years ago by Calvin2077
  2

• long_split issue

  #21 opened 5 years ago by jpaganini
  5

• IOError: [Errno 2] No such file or directory: '/home/a/Desktop/pan-genome-analysis/data/geneCluster/old_clusters_longSplit.txt'

  #59 opened a year ago by faraziAnindo
  1

• panX output file created but it empty?

  #57 opened 2 years ago by neelam19051
  0

• run-TestSet.sh: 25: ./panX.py: Permission denied

  #56 opened 2 years ago by Dimpledavray287
  1

• error running the test set in the py3 branch

  #55 opened 2 years ago by themudo
  0

• Step for generation of archive all_protein_seq.cpk

  #52 opened 2 years ago by GitHublilo
  0

• Failed to export myPangenome's geneCluster.json (step 10)

  #51 opened 2 years ago by jhcuarta
  0

• Could this software uesd in animal?

  #48 opened 3 years ago by ld9866
  2

• Roary output visualization using panX

  #50 opened 3 years ago by leabact
  0

• ValueError

  #49 opened 3 years ago by byeollee
  0

• Fail to run TestSet using panX

  #23 opened 5 years ago by limin321
  11

• PanX visualization: No gene tree

  #47 opened 3 years ago by MarietteEK
  1

• geneCluster & core_geeList.txt output files

  #45 opened 3 years ago by MarietteEK
  0

• Issue with Step-09

  #46 opened 3 years ago by raavan-deka
  0

• Core genome not found even with low soft core parameter in similar genera. Error in step06 & step08

  #42 opened 3 years ago by ashapter
  1

• step 11: ValueError: need more than 1 value to unpack

  #44 opened 3 years ago by NA1919
  0

• step 11 with metadata: IndexError: list index out of range

  #43 opened 3 years ago by NA1919
  0

• docs still state to install miniconda2

  #41 opened 4 years ago by nick-youngblut
  2

• Running workflow for new data

  #40 opened 4 years ago by smb20200615
  0

• Failed to read gbff files

  #39 opened 4 years ago by oeco28
  0

• Long running time or bug?

  #35 opened 4 years ago by Zick007
  2

• DIAMOND fails to produce pairwise alignments in Step 5

  #38 opened 4 years ago by awalling
  0

• Failed to run Test

  #34 opened 4 years ago by stheil15
  3

• Newick

  #18 opened 5 years ago by mdieser
  7

• Biopython Parser Warning

  #37 opened 4 years ago by kbojanic
  0

• xb_xref err

  #36 opened 4 years ago by Bruce-BC
  0

• Roary output for downstream panX pipeline

  #7 opened 6 years ago by wshropshire
  10

• No module Numpy

  #33 opened 5 years ago by pavlohrab
  0

• How to prepare file "stran_list"(step 01) ?

  #32 opened 5 years ago by fengshuo112
  0

• Running sh run-TestSet.sh cause error

  #31 opened 5 years ago by OlegKotcar
  3

• Issue with step 8

  #24 opened 5 years ago by jpaganini
  4

• Very diverse pangenome?

  #30 opened 5 years ago by apredeus
  1

• How strain file should be formatted?

  #29 opened 5 years ago by FilipeMatteoli
  2

• Extracting data for individual genomes

  #28 opened 5 years ago by mdieser
  2

• python3

  #27 opened 5 years ago by JFsanchezherrero
  4

• ete2 missing?

  #13 opened 6 years ago by shlomobl
  4

• Gene gain/loss, duplication

  #20 opened 6 years ago by mdieser
  1

• pan genome visualization component "Sequence Alignment" not working

  #22 opened 5 years ago by wshropshire
  2

• Error step 10

  #19 opened 6 years ago by mdieser
  2

• File input

  #16 opened 6 years ago by mdieser
  6

• Segmentation fault

  #17 opened 6 years ago by pneumowidow
  5

• single copy core genes

  #15 opened 6 years ago by alantsangmb
  4

• Issue with visualization

  #12 opened 6 years ago by pavlo888
  10

• segfault error

  #11 opened 6 years ago by amilesj
  2

• Error in step09: infer presence/absence and gain/loss patterns of all genes

  #10 opened 6 years ago by johanneswerner
  2

• Error in step06: align genes in geneCluster by mafft and build gene trees

  #8 opened 6 years ago by johanneswerner
  5

• The meaning of file name in geneCluster directory

  #6 opened 6 years ago by kaiher
  1

• Support values

  #5 opened 6 years ago by johanneswerner
  1