DessimozLab/read2tree

Issues

• TypeError: cannot unpack non-iterable NoneType object

  #60 opened 7 months ago by pengyan19
  3

• IndexError: tuple index out of range

  #62 opened a month ago by ppat818
  2

• Question: What is the question mark in the amoni acid sequence?

  #63 opened a month ago by YuWang07
  1

• read2tree for NGS

  #66 opened a month ago by Tantoluwa
  1

• Question: generate marker genes from mitochondrion refseq

  #67 opened a month ago by brutal588
  2

• merge-all-mappings fails

  #65 opened 4 months ago by evo-eco-gen
  3

• OMA not generating the marker genes

  #64 opened 4 months ago by evo-eco-gen
  4

• Adding samples to the yeast tree presented in Dylus et al. 2023.

  #61 opened 7 months ago by caonetto
  0

• AttributeError when running OGset.py

  #59 opened 8 months ago by scuadros28
  11

• BUG?: KeyError(s) when running read2tree

  #58 opened 8 months ago by almosnow
  3

• Provide the dna and aa partitions in the output alignment

  #55 opened 9 months ago by ArielRodrig
  1

• TypeError: __init__() takes 2 positional arguments but 3 were given

  #24 opened 2 years ago by marcejuarez90
  3

• for test dataset, tree topology matches but not branch lengths; is this ok?

  #57 opened 10 months ago by douglasgscofield
  2

• Trouble in downloading OMA database

  #56 opened 10 months ago by xuliuouc
  5

• Applied read2tree to customer marker gene sets

  #54 opened 10 months ago by YuWang07
  6

• Can read2tree be run offline and with custom marker gene list?

  #22 opened 2 years ago by masudermann
  3

• QUESTION: Hetero sites.

  #53 opened a year ago by mudymudy
  0

• Adding species but not repeating the mapping of existing species

  #51 opened a year ago by Yuqia
  1

• How to create a tree with bootstrap?

  #52 opened a year ago by sly724
  2

• KeyError in Alignment

  #35 opened a year ago by kodingkoning
  10

• [Question] Are very short insert sizes an issue?

  #37 opened a year ago by mptrsen
  5

• installation error

  #48 opened a year ago by laseulefourmie
  2

• multiple threads for mapping multiple species

  #49 opened a year ago by Yuqia
  4

• Only R1 reads mapped for paired-end read input?

  #50 opened a year ago by Yuqia
  2

• IndexError: list assignment index out of range in Mapper.py

  #46 opened a year ago by bernard-kim
  1

• Error for some reads when conducting mapping step

  #42 opened a year ago by GYQ-form
  4

• Python version

  #43 opened a year ago by Banthandor
  1

• dna_reference not parsed when file extension is not .fa

  #44 opened a year ago by Banthandor
  1

• possible error in the help message of --sample_reads

  #40 opened a year ago by lilindu
  1

• Error message with Conda installation instructions

  #47 opened a year ago by bernard-kim
  1

• RuntimeError: generator raised StopIteration

  #45 opened a year ago by bernard-kim
  0

• cannot get dna from REST

  #41 opened a year ago by GYQ-form
  3

• Installation issue using conda

  #39 opened a year ago by InfiniteLaugh
  2

• can I change the tmp/ path ？

  #38 opened a year ago by LittleFrogHill
  1

• OGs did not have any DNA

  #36 opened a year ago by Alfred-RRu
  4

• UnsatisfiableError when installing from conda

  #32 opened a year ago by kodingkoning
  3

• How to conduct 'Multiple species mode' of read2tree.

  #34 opened a year ago by Galaxy-228
  0

• read2tree can't find corresponding CDS for each OMA group

  #33 opened a year ago by sci-study
  2

• ValueError: fetch called on bamfile without index

  #27 opened a year ago by CJJ8848
  1

• error when map rna-seq to OMA db

  #31 opened a year ago by catslu
  1

• How to add more marker genes

  #28 opened 2 years ago by mudymudy
  10

• bacteria_markergenes also mammalia

  #30 opened 2 years ago by ewaltari
  1

• multiprocessing.pool.RemoteTraceback: KeyError: 'X0022'

  #25 opened 2 years ago by yuanf28
  3

• ete3 install needs changing

  #29 opened 2 years ago by nikishe
  2

• Issue with generating files

  #26 opened 2 years ago by huangjz2
  4

• Installation issue

  #19 opened 2 years ago by dhpalmer
  5

• Error with ngm binary

  #23 opened 2 years ago by 3miumi
  4

• [Question] Marker gene for only one species

  #21 opened 2 years ago by llk578496
  2

• record name cleaning

  #20 opened 2 years ago by M-Zeeb
  2

• (Error) KeyError: 'BETVV'

  #18 opened 2 years ago by shelkmike
  5