naturalis/barcode-constrained-phylogeny

Issues

• Not enough outgroups in geophylogeny

  #116 opened 6 months ago by rvosa
  0

• Broken BCDM

  #115 opened 6 months ago by rvosa
  0

• Attractive visualization

  #105 opened 8 months ago by rvosa
  0

• Provenance tracking, detecting errors

  #107 opened 8 months ago by rvosa
  0

• FAIR, versioned releases of result trees

  #102 opened 8 months ago by rvosa
  0

• Scalability of large subsets

  #100 opened 8 months ago by rvosa
  2

• Assess ITS potential

  #114 opened 7 months ago by rvosa
  0

• Process plant barcodes

  #113 opened 7 months ago by rvosa
  0

• Dynamic parallelization of rule execution

  #99 opened 8 months ago by rvosa
  0

• Scalability of large backbone grafting

  #101 opened 8 months ago by rvosa
  0

• Periodic, automatically scheduled runs

  #103 opened 8 months ago by rvosa
  0

• Software sustainability improvements

  #112 opened 7 months ago by rvosa
  0

• Setup Lepidoptera

  #109 opened 8 months ago by rvosa
  1

• CI/CD and testing

  #110 opened 8 months ago by rvosa
  0

• Better file handling

  #108 opened 8 months ago by rvosa
  0

• Software publishing and visibility

  #106 opened 8 months ago by rvosa
  0

• Variable input species sets

  #104 opened 8 months ago by rvosa
  0

• Reproducibility of conda environments

  #98 opened 8 months ago by rvosa
  0

• Check extreme outliers

  #97 opened 8 months ago by rvosa
  0

• extinct taxa

  #96 opened 8 months ago by rvosa
  0

• Non-flush alignments under certain conditions

  #93 opened 8 months ago by rvosa
  1

• family_fasta refinement needed

  #95 opened 8 months ago by rvosa
  1

• results/fasta/family folder missing

  #90 opened 8 months ago by zahrag
  2

• Curate input data package

  #85 opened 8 months ago by rvosa
  2

• DNA barcode sequence field in BOLD tsv

  #89 opened 8 months ago by zahrag
  4

• makeblastdb.sh shell script not portable

  #86 opened 8 months ago by JWesseling
  8

• Incongruencies in main README

  #87 opened 9 months ago by JWesseling
  2

• create_database.py nucraw to nuc

  #88 opened 9 months ago by AnnemiekeSchonthaler
  2

• Roadmap next release

  #79 opened a year ago by rvosa
  0

• create_database produces inconsistencies

  #83 opened 9 months ago by rvosa
  1

• Create v1.1.0

  #84 opened 10 months ago by rvosa
  3

• Add date/time stamp to log messages

  #80 opened 10 months ago by rvosa
  3

• OpenToL 'broken' taxa

  #81 opened 10 months ago by rvosa
  1

• Picking exemplars

  #77 opened 10 months ago by rvosa
  3

• Outgroup selection with blast

  #82 opened 10 months ago by rvosa
  3

• RAxML placement and branch length optimization

  #75 opened 10 months ago by rvosa
  5

• Submit to WorkflowHub

  #78 opened a year ago by rvosa
  1

• Reroot unrooted raxml subtree

  #76 opened a year ago by rvosa
  1

• Additional indexes needed

  #74 opened a year ago by rvosa
  0

• Implementation status beyond raxml

  #70 opened a year ago by rvosa
  1

• Incompatible dependency graphs across rules

  #72 opened a year ago by rvosa
  1

• hmmalign parameterization

  #67 opened a year ago by rvosa
  1

• Handling empty FASTA files

  #68 opened a year ago by rvosa
  0

• OPTION: Integrate perl tool db into custom db

  #54 opened a year ago by Naomivanes
  1

• Data thinning

  #73 opened a year ago by rvosa
  0

• Spurious pandas dependency errors

  #69 opened a year ago by rvosa
  0

• Skip `temporary_database.db` step

  #71 opened a year ago by rvosa
  0

• Use logging, not print statements

  #53 opened a year ago by rvosa
  0

• raxml with parwise alignments

  #62 opened a year ago by Naomivanes
  2

• MACSE to HMM

  #56 opened a year ago by Naomivanes
  1