Discussions

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  Concatenation of multiple trees

  ramnageena11 asked Sep 3, 2024 in Q&A · Closed · Unanswered

  

  

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  ML and 'AltAll' ancestral FASTA sequences from IQ-TREE .state files

  pdkiser started Sep 25, 2024 in Show and tell

  

  

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  dating a tree with cross bracing

  bonisko started Sep 23, 2024 in General

  

  

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  Ancestral state reconstruction and gaps

  ElizabethRobbins started Sep 17, 2024 in General

  

  

  

  

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  Matching Gene Trees in Treefile to Alignment File Names

  simone-says asked Sep 22, 2024 in Q&A · Unanswered

  

  

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  Assistance Needed with Optimal ML Tree Selection and Sequence Alignment Errors in IQ-TREE2 Analysis

  azhengll asked Sep 21, 2024 in Q&A · Closed · Unanswered

  

  

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  Different tree format for scfl?

  simone-says asked May 31, 2024 in Q&A · Unanswered

  

  

  

  

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  Help with model selection, protein mixture models

  veronicamb started May 20, 2024 in General

  

  

  

  

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  Segmentation fault while running modelfinder in mpi mode

  ycsong started May 2, 2024 in General

  

  

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  Valid (tried-and-tested) combinations of substitution models and rate-heterogeneity across sites models for DNA

  lsjermiin started Jun 8, 2024 in General

  

  

  

  

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  Proposal to remove mention of bootstrap (and other) thresholds from docs

  roblanf started Jun 27, 2024 in General

  

  

  

  

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  How to date trees with date ranges for calibration "points"; confidence intervals

  bonisko started Aug 30, 2024 in General · Closed

  

  

  

  

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  sCF incorrectly mapping values on target tree

  veronicamb asked Aug 23, 2024 in Q&A · Answered

  

  

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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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  Query about the I*R rate-heterogeneity across sites model

  lsjermiin asked Aug 16, 2024 in Q&A · Unanswered

  

  

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  ModelOMatic model selection still supported but not documented?

  lguy asked Aug 13, 2024 in Q&A · Answered

  

  

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  AliSim, codon models and dN/dS values

  thednainus asked Aug 7, 2024 in Q&A · Unanswered

  

  

  

  

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  Sequence order in the input and parallelism affect reproducibility

  apcamargo asked Jun 11, 2024 in Q&A · Answered

  

  

  

  

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  Speeding up iqtree gene trees

  vmkhot asked Jul 31, 2024 in Q&A · Unanswered

  

  

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  IQTREE stopped when Analyzing Big Data

  tenlives asked Aug 3, 2024 in Q&A · Unanswered

  

  

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  Calculation of likelihood ratio (analogous to Bremer support)

  danimelsz asked Aug 3, 2024 in Q&A · Unanswered

  

  

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  How to distinguish UFBoot and SH-aLRT values in an output?

  finwe858 asked Jun 27, 2024 in Q&A · Answered

  

  

  

  

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  Reproducibility with alisim

  tufeiliu started Jul 9, 2024 in General · Closed

  

  

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  trees near ML topology

  diploid2n asked Jul 8, 2024 in Q&A · Unanswered

  

  

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  Constrained tree search not working.

  ghost asked Jul 4, 2024 in Q&A · Closed · Answered

  

  

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