All pull requests

Pull requests

• Skip ';' comment lines before the first FASTA record

  #235·adamjohnwright opened Oct 18, 2026·

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• Fix the distance matrix of partitioned runs, making -fast 3.9x faster

  #234·kevinmoran1988 opened Oct 17, 2026·

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• Make --no-mAIC skip the marginal likelihood again

  #232·kevinmoran1988 opened Oct 17, 2026·

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• Allocate G_matrix only for MCMCTree dating

  #231·kevinmoran1988 opened Oct 16, 2026·

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• Support -mem (memory saving mode) with partition models

  #230·kevinmoran1988 opened Oct 16, 2026·

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• Fix aborts with fused mixture models in multithreaded partitioned runs

  #229·kevinmoran1988 opened Oct 16, 2026·

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• Fix uninitialized model weights in the partitioned .iqtree report

  #228·kevinmoran1988 opened Oct 16, 2026·

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• Fix heap buffer overflow with +ASC_MIS/+ASC_INF in edge-linked partitions

  #226·kevinmoran1988 opened Oct 16, 2026·

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• Add extant sequence reconstruction (-esr) and gap-aware ASR/ESR (-gap-asr, -gap-esr)

  #223·trongnhanuit opened Sep 25, 2026Member·

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• Fix MixtureFinder error messages

  #222·HS6986 opened Sep 21, 2026Contributor·

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• Fix a bug about mAIC log file output #218

  #220·HuaiyanRen opened Sep 18, 2026Collaborator·

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• Fix integer overflow when computing distance matrices

  #217·Thomas1664 opened Sep 12, 2026·

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• SH-aLRT: draw RELL replicates as bootstrap samples whatever -j/-J selected (#198)

  #214·cindykrafft opened Sep 9, 2026·

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• Fix submodel indexing logic in ModelMarkov functions, fix likelihood calculations in AlignmentPairwise

  #194·StefanFlaumberg opened Jul 29, 2026Contributor·

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• Introduce --site(-float)-weights options and implement Bayesian Bootstrap

  #157·trongnhanuit opened May 5, 2026Member·

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• PMSR model implementation

  #40·StefanFlaumberg opened May 19, 2025Contributor·

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