Issues

• Possible confusion about the -s formula in the User Guide

  weizhongli/cdhit#152 · Filter by author alyzart22 opened on Jul 31, 2026

• Ambiguous nucleotides

  weizhongli/cdhit#151 · Filter by author irenekaregi opened on Dec 11, 2025
  1

• Malicious links in docs/comments/wiki/README

  weizhongli/cdhit#149 · Filter by author benjaminhwilliams opened on Aug 26, 2025

• More clusters from hierarchical clustering than direct 30% CD-HIT run

  weizhongli/cdhit#148 · Filter by author Gabriel-QIN opened on Jul 8, 2025

• Sequence decription not showing despite -d 0 flag

  weizhongli/cdhit#147 · Filter by author stefan-rooke opened on Mar 20, 2025
  1

• cd-hit-2d excluding from clusters good aligments

  weizhongli/cdhit#146 · Filter by author laugior opened on May 14, 2024

• Sort fasta by cluster size not working

  weizhongli/cdhit#145 · Filter by author kgun12 opened on Apr 28, 2024

• Running Cd Hit is slow

  weizhongli/cdhit#144 · Filter by author mdMoinuddinSheam opened on Mar 24, 2024

• s option for sequence overlapping threshold picking up wrong cut-off values

  weizhongli/cdhit#143 · Filter by author yuqiwangcbcb opened on Mar 6, 2024

• Comparing sequences from 0 to 0!help!

  weizhongli/cdhit#142 · Filter by author Eager144000 opened on Dec 21, 2023
  3

• unknown warning when installing cd-hit, issue?

  weizhongli/cdhit#141 · Filter by author Robvh-git opened on Oct 13, 2023
  1

• cd-hit installation

  weizhongli/cdhit#140 · Filter by author fa-rahimzadeh opened on Sep 10, 2023
  1

• cd-hit-dup Segmentation fault (core dumped)

  weizhongli/cdhit#139 · Filter by author scross92 opened on Aug 23, 2023
  5

• clstr2txt.pl

  weizhongli/cdhit#138 · Filter by author SaidaSaad opened on May 18, 2023

• bash: cd-hit: command not found...

  weizhongli/cdhit#137 · Filter by author zhenyaliu77 opened on Mar 10, 2023
  3

• How to dealing with big gene dataset?

  weizhongli/cdhit#136 · Filter by author B-1991-ing opened on Jan 26, 2023
  4

• What is the bandwidth option?

  weizhongli/cdhit#135 · Filter by author alexzord opened on Jan 17, 2023

• cd-hit-est -d description length option not working

  weizhongli/cdhit#134 · Filter by author Vicbuz opened on Dec 1, 2022
  1

• problem with maximum allowed sequences lengths

  weizhongli/cdhit#133 · Filter by author Valentin-Bio-zz opened on Nov 16, 2022

• How can cd-hit-est-2d allow 80% cutoff

  weizhongli/cdhit#131 · Filter by author luhan125 opened on Sep 20, 2022

• print alignment -p 1 not work

  weizhongli/cdhit#130 · Filter by author jianshu93 opened on Sep 1, 2022

• How to reset MAX_SEQ

  weizhongli/cdhit#129 · Filter by author timeresistance1996 opened on Jun 20, 2022
  3

• Problems during running PSI-CD-HIT:Name "main::bl_dir" used only once: possible typo at ./psi-cd-hit.pl line 103.

  weizhongli/cdhit#128 · Filter by author AL-Yan opened on May 18, 2022
  6

• Where is psi-cd-hit?

  weizhongli/cdhit#127 · Filter by author iquasere opened on Apr 12, 2022

• FATAL docker build error

  weizhongli/cdhit#126 · Filter by author steph-birnbaum opened on Mar 16, 2022
  1