Issues

• gene_markers_identification crashed

  biobakery/phylophlan#124 · Filter by author jiaojiaoguan opened on Mar 19, 2025
  2

  

• Refine_gene_tree crashed

  biobakery/phylophlan#123 · Filter by author Valentin-Bio opened on Mar 1, 2025

• Blastp-error

  biobakery/phylophlan#122 · Filter by author mengyuan-JI opened on Feb 20, 2025

• Running partial workflow

  biobakery/phylophlan#121 · Filter by author AroneyS opened on Jan 17, 2024
  1

  

• Trouble running example 2 - Tree of Life

  biobakery/phylophlan#120 · Filter by author sierra-smith opened on Dec 1, 2023

• The generated phylogenetic tree is missing MAGs at the leaf nodes.

  biobakery/phylophlan#119 · Filter by author ylei14 opened on Nov 25, 2023

• broken link on wiki

  biobakery/phylophlan#118 · Filter by author jorondo1 opened on Nov 16, 2023

• Reducing number of RAxML threads to 20, as it appears to underperform with more threads

  help wanted
  biobakery/phylophlan#117 · Filter by author ylei14 opened on Nov 11, 2023
  2

  

• What is the difference between "phylophlan" database and "SGB.XXX"?

  biobakery/phylophlan#116 · Filter by author augfranco93 opened on Oct 3, 2023
  2

• [e] gene_markers_identification crashed

  biobakery/phylophlan#115 · Filter by author kaw97 opened on Sep 19, 2023
  1

  

• RAxML can't parse alignments for which there are sequences made entirely of undetermined characters

  biobakery/phylophlan#113 · Filter by author RyanCook94 opened on Jun 30, 2023
  1

• UnboundLocalError: cannot access local variable 'uniprotkb2uniref90' where it is not associated with a value

  biobakery/phylophlan#111 · Filter by author chennyhui opened on May 28, 2023

• maybee update taxa2core_cpa* to recent uniprot release

  biobakery/phylophlan#109 · Filter by author EricDeveaud opened on May 11, 2023

• [e] No alignments found to concatenate

  biobakery/phylophlan#104 · Filter by author jwkkang opened on Feb 24, 2023
  1

  

• Phylophlan Error

  biobakery/phylophlan#103 · Filter by author afedynak opened on Feb 16, 2023
  3

  

• FastTreeMP returned non-zero exit status 1.

  biobakery/phylophlan#102 · Filter by author gabridinosauro opened on Oct 21, 2022
  8

  

• mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')

  biobakery/phylophlan#101 · Filter by author PabloArrow opened on Oct 19, 2022
  1

  

• Error: returned non-zero exit status 2

  biobakery/phylophlan#99 · Filter by author GriffyGe opened on Sep 11, 2022
  1

  

• Bootstrap error obtained. zsh: killed

  biobakery/phylophlan#97 · Filter by author pavlo888 opened on Aug 12, 2022
  1

  

• set.py long description file name variation

  biobakery/phylophlan#95 · Filter by author erinpnewcomer opened on Jul 7, 2022
  1

  

• uniprot database differing number of markers

  biobakery/phylophlan#93 · Filter by author pavlo888 opened on Jun 20, 2022
  4

  

• Error while running S aureus example

  biobakery/phylophlan#92 · Filter by author rajneeshdadwal opened on Jun 20, 2022
  1

  

• where is the log file

  biobakery/phylophlan#90 · Filter by author pavlo888 opened on May 25, 2022
  3

  

• Error running Phylophlan

  biobakery/phylophlan#88 · Filter by author rybioinf opened on Apr 16, 2022
  3

  

• Feature proposal: tqdm progressbar during execution of phylophlan

  enhancement
  biobakery/phylophlan#85 · Filter by author valentynbez opened on Mar 29, 2022