Discussions

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  Ensuring Convergence

  tsbernat asked Feb 5, 2026 in Q&A · Unanswered

  

  

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  Running CAFE5 on large tree

  ToriEggers asked Feb 20, 2026 in Q&A · Unanswered

  

  

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  Interpretation of results "Gamma_family_likelihoods.txt"

  EmilianoMora asked Aug 19, 2025 in Q&A · Answered

  

  

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  Definition of gene family

  norahuang885-glitch asked Jan 28, 2026 in Q&A · Answered

  

  

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  Failed to initialize any reasonable values

  marimaro asked Feb 16, 2021 in Q&A · Answered

  

  

  

  

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  Question about interpreting 'Final Likelihood (-lnL)' and when to use --poisson in CAFE5

  MegadogDede asked Jan 13, 2026 in Q&A · Unanswered

  

  

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  How to annotate expanded/extracted gene families?

  Ruiqi-CUB asked Feb 24, 2023 in Q&A · Unanswered

  

  

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  Species not found in gene family

  arunsethuraman asked Mar 23, 2021 in Q&A · Answered

  

  

  

  

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  Simulation Abnormality

  danielagandrade asked Nov 11, 2025 in Q&A · Unanswered

  

  

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  How should I analyze a gene family that does not exist in the outgroup?

  Eika728 asked Nov 19, 2025 in Q&A · Answered

  

  

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  Subfamilies as a way to resolve too large families

  MirkMart asked Nov 20, 2025 in Q&A · Answered

  

  

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  Some species have 0 contracted and expanded gene families

  yuanw-18 asked Feb 26, 2025 in Q&A · Answered

  

  

  

  

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  Extreme OG size variation - definition

  Dayana-Turquetti asked Oct 3, 2025 in Q&A · Answered

  

  

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  Failed to reconstruct 1 families

  walkyshitake asked Sep 12, 2025 in Q&A · Unanswered

  

  

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  extremely small difference between max and min counts issue

  Taoping-Wu asked Aug 13, 2025 in Q&A · Answered

  

  

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  Model Questions and Missing Information on Tutorial

  danielagandrade asked Jul 31, 2025 in Q&A · Answered

  

  

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  The lambda tree structure does not match that of the tree

  austinchipps asked Jul 22, 2025 in Q&A · Answered

  

  

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  Wrong number of expansion or contraction Orthogroups

  njliangdong asked Apr 1, 2025 in Q&A · Answered

  

  

  

  

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  cafe k value

  LN-11 asked Jun 28, 2025 in Q&A · Answered

  

  

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  Input species tree nodes don't match output Base_clade_results.txt nodes

  lilypeck asked Jul 9, 2025 in Q&A · Unanswered

  

  

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  Clarification on Family vs Branch-Level Significance in CAFE5 Outputs

  meeranhussain asked Jun 12, 2025 in Q&A · Answered

  

  

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  Subject: Assistance with CAFE5: High Failure Rates for Gene Families with k=2

  Jiahe-Sun asked Apr 16, 2025 in Q&A · Answered

  

  

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  After multiple cycles of deleting families, rerunning cafe5 still reports errors.

  guo23e asked Apr 15, 2025 in Q&A · Answered

  

  

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  new error: The following families had failure rates

  LiS-88 asked Nov 6, 2022 in Q&A · Answered

  

  

  

  

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  found in gene family

  guo23e asked Apr 14, 2025 in Q&A · Answered

  

  

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