Discussions

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  Rescaling during support mapping unclear

  bmichanderson asked Feb 20, 2026 in Q&A · Answered

  

  

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  different branch IDs in gcf and scfl for the same species tree

  HiranyaSudasinghe asked Jul 23, 2025 in Q&A · Unanswered

  

  

  

  

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  How to use an outgroup clade in ASR

  ga01 started Mar 3, 2026 in General

  

  

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  Linking non-reversible exchangeabilities (NONREV) across frequency profiles

  kr3118 started Feb 27, 2026 in Ideas

  

  

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  Partition merging .best_model format issues

  zivlie asked Oct 14, 2025 in Q&A · Unanswered

  

  

  

  

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  IQTREE handling indels

  sammadge asked Feb 6, 2026 in Q&A · Unanswered

  

  

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  outgroup in ancestral sequence reconstruction

  ga01 started Feb 2, 2026 in General

  

  

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  -m MFP = default?

  BjoernStelbrink asked Dec 18, 2025 in Q&A · Unanswered

  

  

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  Unexpected behavior in IQ-TREE 3.0.1

  mmatschiner asked Jan 19, 2026 in Q&A · Unanswered

  

  

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  IQTREE Web Server crash

  wangjianpeng847-gif asked Jan 12, 2026 in Q&A · Unanswered

  

  

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  Having a challange to compare models for snp phylogenetic inference

  henok-bot asked Jan 7, 2026 in Q&A · Unanswered

  

  

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  Parameter -o for setting outgroup is not working and I'm getting a long branch for the first species (IQTree2.3.4)

  badiaclara asked Nov 10, 2024 in Q&A · Answered

  

  

  

  

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  Using IQ-TREE for distance computation

  apcamargo asked Dec 19, 2025 in Q&A · Unanswered

  

  

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  PMSF on Partitioned Data

  kr3118 asked Nov 23, 2025 in Q&A · Unanswered

  

  

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  IQTREE Web Server crash?

  hsutingwei17 asked Nov 4, 2025 in Q&A · Unanswered

  

  

  

  

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  symtest output file names

  zivlie asked Oct 20, 2025 in Q&A · Unanswered

  

  

  

  

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  Beginner's Question: Rooting Phylogenies to proceed with IQ2MC workflow

  walkyshitake asked Oct 29, 2025 in Q&A · Unanswered

  

  

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  Testing only a few rooting positions

  jsoghigian asked Oct 29, 2025 in Q&A · Unanswered

  

  

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  IQTREE PMSF crash

  erikrikarddaniel started Oct 22, 2025 in General

  

  

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  Way to "silence" Identifying sites to remove...?

  jsoghigian asked Oct 19, 2025 in Q&A · Unanswered

  

  

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  Branch lengths of combined morph+genetic analyses

  DeondeJager asked Sep 29, 2025 in Q&A · Closed · Answered

  

  

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  Alisim: Only simulate InDels in existing sequence / Enable more complex dN/dS codon models

  casparbein asked Sep 24, 2025 in Q&A · Unanswered

  

  

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  iqtree3 "site-freq" option: name clash in the context of AliSim and Mixture models under PMSF

  danieltamarit started Sep 18, 2025 in General

  

  

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  Plotting bootstrap values on a tree using a file with bootstrap replicates

  veronicamb asked Aug 21, 2024 in Q&A · Closed · Answered

  

  

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  Initialise model parameters from user-defined values

  kr3118 started Sep 2, 2025 in Ideas

  

  

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