Issues

• Numerical instability in to_independent_model

  debbiemarkslab/EVcouplings#339 · Filter by author aaronkollasch opened on Jun 22, 2026
  1

• Using complex model to test coevolution – how to interpret _ECs.txt?

  debbiemarkslab/EVcouplings#337 · Filter by author C-grapes opened on May 28, 2026

• Pandas>=3 breaking change in compare stage

  debbiemarkslab/EVcouplings#335 · Filter by author kpgbrock opened on Apr 3, 2026

• TypeError in LogisticRegression for scikit-learn v1.8+

  debbiemarkslab/EVcouplings#334 · Filter by author rfhaque opened on Mar 6, 2026
  1

  

• pkg_resources becoming deprecated

  debbiemarkslab/EVcouplings#328 · Filter by author samberry19 opened on Jul 8, 2025
  1

  

• Evolutionary coupling score from AlphaFold Multimer prediction

  debbiemarkslab/EVcouplings#323 · Filter by author maclandrol opened on Feb 19, 2025
  1

• Running evcouplings on a cluster without network access

  debbiemarkslab/EVcouplings#322 · Filter by author ld139 opened on Dec 11, 2024
  6

• SIFTS

  debbiemarkslab/EVcouplings#298 · Filter by author t9lex opened on Jul 21, 2023
  4

• Complex Pipeline still Coupling Successful, but after ended with an runtime error

  debbiemarkslab/EVcouplings#297 · Filter by author Prasanth-Kumar87 opened on Jun 23, 2023

• KeyError: 'samples' using complex pipeline

  debbiemarkslab/EVcouplings#285 · Filter by author kirannazarali opened on Feb 8, 2023
  3

• Incorporate hhpred for pdb search in compare stage

  feature
  debbiemarkslab/EVcouplings#276 · Filter by author kpgbrock opened on Apr 26, 2022

• lack of explicit separator in read_csv in /mutate/protocol.py

  enhancement
  debbiemarkslab/EVcouplings#272 · Filter by author paulaberry opened on Feb 3, 2022
  3

• Non-alphabet characters aren't counted as gaps when computing sequence coverage

  enhancement
  debbiemarkslab/EVcouplings#268 · Filter by author nikkithadani opened on Nov 9, 2021
  1

  

• Unable to perform the de novo protein structure prediction.

  debbiemarkslab/EVcouplings#266 · Filter by author sebel76 opened on Apr 29, 2021
  2

• Add 2ndary structure pred. from ECs

  enhancementhelp wanted
  debbiemarkslab/EVcouplings#264 · Filter by author njrollins opened on Apr 19, 2021

• Add alignment summary: organisms

  enhancementhelp wanted
  debbiemarkslab/EVcouplings#263 · Filter by author njrollins opened on Apr 19, 2021
  1

• Add statistics about filtered sequences to output

  feature
  debbiemarkslab/EVcouplings#262 · Filter by author thomashopf opened on Apr 7, 2021
  

• CouplingsScoresCompared_longrange.csv misses couplings

  debbiemarkslab/EVcouplings#252 · Filter by author ddingding opened on Oct 7, 2020
  4

• Computation of N_eff when the align stage (but not the couplings stage) is run

  enhancement
  debbiemarkslab/EVcouplings#251 · Filter by author berkalpay opened on Oct 7, 2020
  3

  

• Add 'existing paired alignment' to complex pipeline

  enhancementfeature
  debbiemarkslab/EVcouplings#247 · Filter by author njrollins opened on Aug 7, 2020
  2

• evcomplex scoring model

  debbiemarkslab/EVcouplings#234 · Filter by author cross12tamu opened on Apr 17, 2020
  6

• Output alignment file sorted by sequence identity

  enhancement
  debbiemarkslab/EVcouplings#226 · Filter by author kpgbrock opened on Oct 28, 2019

• More flexible sequence weight handling

  enhancement
  debbiemarkslab/EVcouplings#224 · Filter by author thomashopf opened on Aug 9, 2019

• Add MMseqs2 as align protocol

  featureprio: low
  debbiemarkslab/EVcouplings#218 · Filter by author sacdallago opened on Jun 25, 2019
  1

• InvalidParameterError: provided annotation file has no annotation information

  complexenhancementwontfix
  debbiemarkslab/EVcouplings#214 · Filter by author sacdallago opened on Apr 2, 2019
  3