{"id":43647,"name":"iqtree3","ecosystem":"submodules","repository_url":null,"issues_count":8,"created_at":"2025-06-18T05:22:52.552Z","updated_at":"2025-06-18T05:22:52.552Z","purl":"pkg:submodules/iqtree3","unique_repositories_count":1,"unique_repositories_count_past_30_days":1,"recent_issues":[{"uuid":"3752242653","node_id":"PR_kwDOLrtbes66D4ks","number":393,"state":"open","title":"Bump iqtree3 from `9341251` to `c276222`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":null,"state_reason":null,"created_at":"2025-12-22T04:11:14.000Z","updated_at":"2025-12-22T04:29:23.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`9341251`","new_version":"`c276222`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `9341251` to `c276222`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/c2762220d0f71e048dc1944df8b10acb295e45a4\"\u003e\u003ccode\u003ec276222\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/119\"\u003e#119\u003c/a\u003e from etw35/patch-1\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/c5c5c0a6f34fb92cded390e3f4f1adf095cfe62e\"\u003e\u003ccode\u003ec5c5c0a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/115\"\u003e#115\u003c/a\u003e from trongnhanuit/funDi_fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/fb25a0fb2fa5fc59f86be0446f2efafd0b6560fb\"\u003e\u003ccode\u003efb25a0f\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/105\"\u003e#105\u003c/a\u003e from taranehkhosrojerdi/weighted-perturbation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/48fd76847707da6d6dfbd5ce44e3390686f3e80c\"\u003e\u003ccode\u003e48fd768\u003c/code\u003e\u003c/a\u003e Update phylotesting.cpp\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/387184c7718b1ebeadeedacc0ffc6c06599ae41b\"\u003e\u003ccode\u003e387184c\u003c/code\u003e\u003c/a\u003e Improve the optimization of rho (of the FunDi model)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/dbc1c778356a33ede7c599852e851a51fdd75c55\"\u003e\u003ccode\u003edbc1c77\u003c/code\u003e\u003c/a\u003e add weighted perturbation\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/93412518a00c48066bda6795b5709214b7bf8eb5...c2762220d0f71e048dc1944df8b10acb295e45a4\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/393","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/393","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/393/packages"},{"uuid":"3471958508","node_id":"PR_kwDOLrtbes6reI2q","number":329,"state":"open","title":"Bump iqtree3 from `a6739a1` to `1cda777`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-10-01T04:20:34.000Z","updated_at":"2025-10-01T04:36:45.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`a6739a1`","new_version":"`1cda777`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `a6739a1` to `1cda777`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/1cda77774361aac0cb152047f3d1d7c124499cea\"\u003e\u003ccode\u003e1cda777\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/11\"\u003e#11\u003c/a\u003e from HS6986/feature/HS6986/extend-MixtureFinder\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/df4c9ee465b16cb65e9c208e143dd9805cedea34\"\u003e\u003ccode\u003edf4c9ee\u003c/code\u003e\u003c/a\u003e update latest cmake\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/9578f2b6186aab8ba83740d41f0aa501e0193707\"\u003e\u003ccode\u003e9578f2b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/83\"\u003e#83\u003c/a\u003e from thomaskf/Ali_Taba\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/1e9303fdd449390ddf5d29a8c7cd84d783f6e457\"\u003e\u003ccode\u003e1e9303f\u003c/code\u003e\u003c/a\u003e Merge branch 'master' into feature/HS6986/extend-MixtureFinder\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/760433a85bd28583b12a807718c6f972accd33bd\"\u003e\u003ccode\u003e760433a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/29\"\u003e#29\u003c/a\u003e from IntegerLimit/mr-bayes-support-iqtree-3\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/6c6f9781f8e9b564b69c9cc344f83500d373be01\"\u003e\u003ccode\u003e6c6f978\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/73\"\u003e#73\u003c/a\u003e from StefanFlaumberg/bugfix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/28c89a58f0f96d41f3e707e7e271e3ddaa5306f1\"\u003e\u003ccode\u003e28c89a5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/75\"\u003e#75\u003c/a\u003e from Hashara/gitworkflow-memcheck\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/05983b5c641071b72ee1c8f91b658e482166e839\"\u003e\u003ccode\u003e05983b5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/76\"\u003e#76\u003c/a\u003e from magnified103/patch-1\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/46c3bf76316073d7b8267556193637e55c5d35c3\"\u003e\u003ccode\u003e46c3bf7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/88\"\u003e#88\u003c/a\u003e from trongnhanuit/alisim_bug_fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f7de1bba65819a6a77fcd220f60be75c9987b6a5\"\u003e\u003ccode\u003ef7de1bb\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/81\"\u003e#81\u003c/a\u003e from iqtree/nhan_auto_switch_pars\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/a6739a16530eec695ab85144db5c9b83abe77074...1cda77774361aac0cb152047f3d1d7c124499cea\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/329","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/329","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/329/packages"},{"uuid":"2872832326","node_id":"PR_kwDOLrtbes6rO_FG","number":328,"state":"open","title":"Bump iqtree3 from `a6739a1` to `760433a`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-30T04:17:01.000Z","updated_at":"2025-09-30T04:17:02.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`a6739a1`","new_version":"`760433a`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `a6739a1` to `760433a`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/760433a85bd28583b12a807718c6f972accd33bd\"\u003e\u003ccode\u003e760433a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/29\"\u003e#29\u003c/a\u003e from IntegerLimit/mr-bayes-support-iqtree-3\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/6c6f9781f8e9b564b69c9cc344f83500d373be01\"\u003e\u003ccode\u003e6c6f978\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/73\"\u003e#73\u003c/a\u003e from StefanFlaumberg/bugfix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/28c89a58f0f96d41f3e707e7e271e3ddaa5306f1\"\u003e\u003ccode\u003e28c89a5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/75\"\u003e#75\u003c/a\u003e from Hashara/gitworkflow-memcheck\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/05983b5c641071b72ee1c8f91b658e482166e839\"\u003e\u003ccode\u003e05983b5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/76\"\u003e#76\u003c/a\u003e from magnified103/patch-1\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/46c3bf76316073d7b8267556193637e55c5d35c3\"\u003e\u003ccode\u003e46c3bf7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/88\"\u003e#88\u003c/a\u003e from trongnhanuit/alisim_bug_fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f7de1bba65819a6a77fcd220f60be75c9987b6a5\"\u003e\u003ccode\u003ef7de1bb\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/81\"\u003e#81\u003c/a\u003e from iqtree/nhan_auto_switch_pars\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/df6e521a012360898f47f393889236512e0b0014\"\u003e\u003ccode\u003edf6e521\u003c/code\u003e\u003c/a\u003e Update Help Comment: Model is Always Outputted\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f462794b0afd9d847140c7445801185a567a3cd2\"\u003e\u003ccode\u003ef462794\u003c/code\u003e\u003c/a\u003e Protein: Fix Missing Endline\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/50ff3bc5370a11ae3d6060073d38a9c39600f515\"\u003e\u003ccode\u003e50ff3bc\u003c/code\u003e\u003c/a\u003e Protein: Fully Remove GTR Rate Matrix Logic\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f1be77779a0de3036f45297d349fc1f2d036fc4a\"\u003e\u003ccode\u003ef1be777\u003c/code\u003e\u003c/a\u003e Comment: Update Fallback Model for Protein\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/a6739a16530eec695ab85144db5c9b83abe77074...760433a85bd28583b12a807718c6f972accd33bd\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/328","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/328","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/328/packages"},{"uuid":"3455900794","node_id":"PR_kwDOLrtbes6qoLIR","number":323,"state":"open","title":"Bump iqtree3 from `7cded0c` to `a6739a1`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":5,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-26T06:00:13.000Z","updated_at":"2025-09-27T08:01:27.782Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`7cded0c`","new_version":"`a6739a1`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `7cded0c` to `a6739a1`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/a6739a16530eec695ab85144db5c9b83abe77074\"\u003e\u003ccode\u003ea6739a1\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/93\"\u003e#93\u003c/a\u003e from thomaskf/libiqtree\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/722c99460799551977ecc9549dfe238fced563f8\"\u003e\u003ccode\u003e722c994\u003c/code\u003e\u003c/a\u003e Allow the fix the branch length as the input tree when fixing the tree for li...\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/7cded0cbc1767dab82bed39720a809f9359d7227...a6739a16530eec695ab85144db5c9b83abe77074\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/323","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/323","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/323/packages"},{"uuid":"2627677398","node_id":"PR_kwDOLrtbes6cnyzW","number":264,"state":"open","title":"Bump iqtree3 from `993275d` to `7cded0c`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-30T04:02:45.000Z","updated_at":"2025-06-30T04:02:45.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`993275d`","new_version":"`7cded0c`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `993275d` to `7cded0c`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/7cded0cbc1767dab82bed39720a809f9359d7227\"\u003e\u003ccode\u003e7cded0c\u003c/code\u003e\u003c/a\u003e allow running CI workflow on push with every branch\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/5b2cf2468deb56a09c1e60ee5c96754bc2aa03c5\"\u003e\u003ccode\u003e5b2cf24\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/68\"\u003e#68\u003c/a\u003e from iqtree/huaiyan\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/5eb1253a15e4f1b1652b4f6a7aa4b470a904a0df\"\u003e\u003ccode\u003e5eb1253\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/71\"\u003e#71\u003c/a\u003e from thomaskf/unit_test_update\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/dcab2d0bffa41bda488202aab6ab4bfad0bf8e13\"\u003e\u003ccode\u003edcab2d0\u003c/code\u003e\u003c/a\u003e notify about auto-detect seq type for both single and partition model. mAIC d...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/48c034227fd12d0544422a189f73bc9d06ef1758\"\u003e\u003ccode\u003e48c0342\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/13\"\u003e#13\u003c/a\u003e from Hashara/unit_test_update\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/a4cff0a1f00379ba77a5fc3aa6f4f3e539cbd19f\"\u003e\u003ccode\u003ea4cff0a\u003c/code\u003e\u003c/a\u003e increase runtime threshold\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/9abfdc539c2c9c641fd7e0cfb3d1a634fe9f9563\"\u003e\u003ccode\u003e9abfdc5\u003c/code\u003e\u003c/a\u003e increase runtime threshold\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/6d12a9523e35f3151f2c770f153ccb9be40109ca\"\u003e\u003ccode\u003e6d12a95\u003c/code\u003e\u003c/a\u003e increase runtime threshold\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/8f5f22a063cae6f1f62dcb1b1fea51fbb483b2bf\"\u003e\u003ccode\u003e8f5f22a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/12\"\u003e#12\u003c/a\u003e from Hashara/unit_test_update\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/96de033d2ca661bcd3164ccd440410e4dd470c2a\"\u003e\u003ccode\u003e96de033\u003c/code\u003e\u003c/a\u003e add unit_test_update branch trigger to the workflow\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/993275d52e10dc026840b7028048c7e517c21e82...7cded0cbc1767dab82bed39720a809f9359d7227\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/264","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/264","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/264/packages"},{"uuid":"3166734741","node_id":"PR_kwDOLrtbes6blyjA","number":247,"state":"open","title":"Bump iqtree3 from `d9bc0a6` to `ce5b6ce`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":3,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-23T04:33:24.000Z","updated_at":"2025-06-23T06:11:39.334Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`d9bc0a6`","new_version":"`ce5b6ce`","repository_url":"https://github.com/thomaskf/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/thomaskf/iqtree3) from `d9bc0a6` to `ce5b6ce`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/ce5b6ceae081bffc41d433b48c7a60575211e004\"\u003e\u003ccode\u003ece5b6ce\u003c/code\u003e\u003c/a\u003e Revert \u0026quot;Move the line \u0026quot;Optimizing NNI: done...\u0026quot; to the medium verbose mode\u0026quot;\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/a39bbadbbc26ac299d621297e3eb69e6d94fa6cc\"\u003e\u003ccode\u003ea39bbad\u003c/code\u003e\u003c/a\u003e Move the line \u0026quot;Optimizing NNI: done...\u0026quot; to the medium verbose mode\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/thomaskf/iqtree3/compare/d9bc0a64e4a905b802193f418bba69a2ec1a6e54...ce5b6ceae081bffc41d433b48c7a60575211e004\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/247","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/247","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/247/packages"},{"uuid":"2610157613","node_id":"PR_kwDOLrtbes6bk9gt","number":246,"state":"open","title":"Bump iqtree3 from `1357e36` to `d9bc0a6`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-23T01:42:38.000Z","updated_at":"2025-06-23T01:42:39.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`1357e36`","new_version":"`d9bc0a6`","repository_url":"https://github.com/thomaskf/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/thomaskf/iqtree3) from `1357e36` to `d9bc0a6`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/d9bc0a64e4a905b802193f418bba69a2ec1a6e54\"\u003e\u003ccode\u003ed9bc0a6\u003c/code\u003e\u003c/a\u003e Modify the consensus tree function for iqtree library for strict consensus tree\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/thomaskf/iqtree3/compare/1357e3646cf3d51cab75f13562575cf937d67702...d9bc0a64e4a905b802193f418bba69a2ec1a6e54\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/246","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/246","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/246/packages"},{"uuid":"3155431174","node_id":"PR_kwDOLrtbes6bADSp","number":239,"state":"open","title":"Bump iqtree3 from `f7660f4` to `1357e36`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-18T04:32:46.000Z","updated_at":"2025-06-18T04:59:13.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`f7660f4`","new_version":"`1357e36`","repository_url":"https://github.com/thomaskf/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/thomaskf/iqtree3) from `f7660f4` to `1357e36`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/1357e3646cf3d51cab75f13562575cf937d67702\"\u003e\u003ccode\u003e1357e36\u003c/code\u003e\u003c/a\u003e Merge branch 'mixFinder_update' into libiqtree\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/fc0d98452e31baf099b936d67f3f6c25af375d43\"\u003e\u003ccode\u003efc0d984\u003c/code\u003e\u003c/a\u003e Fixed the incorrect usage of ASSERT\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/d6c1f5b5843083cf0a04bfdfa97cbe9ce22f7652\"\u003e\u003ccode\u003ed6c1f5b\u003c/code\u003e\u003c/a\u003e Added the verification on the initial likelihood value after mixtureFinder\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/0743b7ad0cde1c2c544a3ff89d41e2584cf2db96\"\u003e\u003ccode\u003e0743b7a\u003c/code\u003e\u003c/a\u003e Fixed the different RHAS parameters and branch lengths between the MixFinder ...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/c2eab2f788f68db03cc0bc2208563baf2085fcba\"\u003e\u003ccode\u003ec2eab2f\u003c/code\u003e\u003c/a\u003e Remove the increase of the maximum number of iterations for mixture model\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/thomaskf/iqtree3/compare/f7660f4d53f9900c867e1be985e8c98112f6b764...1357e3646cf3d51cab75f13562575cf937d67702\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/239","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/239","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/239/packages"}],"issue_packages":[{"old_version":"`9341251`","new_version":"`c276222`","update_type":null,"path":null,"pr_created_at":"2025-12-22T04:11:14.000Z","version_change":"`9341251` → `c276222`","issue":{"uuid":"3752242653","node_id":"PR_kwDOLrtbes66D4ks","number":393,"state":"open","title":"Bump iqtree3 from `9341251` to `c276222`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":null,"state_reason":null,"created_at":"2025-12-22T04:11:14.000Z","updated_at":"2025-12-22T04:29:23.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`9341251`","new_version":"`c276222`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `9341251` to `c276222`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/c2762220d0f71e048dc1944df8b10acb295e45a4\"\u003e\u003ccode\u003ec276222\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/119\"\u003e#119\u003c/a\u003e from etw35/patch-1\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/c5c5c0a6f34fb92cded390e3f4f1adf095cfe62e\"\u003e\u003ccode\u003ec5c5c0a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/115\"\u003e#115\u003c/a\u003e from trongnhanuit/funDi_fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/fb25a0fb2fa5fc59f86be0446f2efafd0b6560fb\"\u003e\u003ccode\u003efb25a0f\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/105\"\u003e#105\u003c/a\u003e from taranehkhosrojerdi/weighted-perturbation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/48fd76847707da6d6dfbd5ce44e3390686f3e80c\"\u003e\u003ccode\u003e48fd768\u003c/code\u003e\u003c/a\u003e Update phylotesting.cpp\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/387184c7718b1ebeadeedacc0ffc6c06599ae41b\"\u003e\u003ccode\u003e387184c\u003c/code\u003e\u003c/a\u003e Improve the optimization of rho (of the FunDi model)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/dbc1c778356a33ede7c599852e851a51fdd75c55\"\u003e\u003ccode\u003edbc1c77\u003c/code\u003e\u003c/a\u003e add weighted perturbation\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/93412518a00c48066bda6795b5709214b7bf8eb5...c2762220d0f71e048dc1944df8b10acb295e45a4\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/393","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/393","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/393/packages"}},{"old_version":"`a6739a1`","new_version":"`1cda777`","update_type":null,"path":null,"pr_created_at":"2025-10-01T04:20:34.000Z","version_change":"`a6739a1` → `1cda777`","issue":{"uuid":"3471958508","node_id":"PR_kwDOLrtbes6reI2q","number":329,"state":"open","title":"Bump iqtree3 from `a6739a1` to `1cda777`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-10-01T04:20:34.000Z","updated_at":"2025-10-01T04:36:45.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`a6739a1`","new_version":"`1cda777`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `a6739a1` to `1cda777`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/1cda77774361aac0cb152047f3d1d7c124499cea\"\u003e\u003ccode\u003e1cda777\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/11\"\u003e#11\u003c/a\u003e from HS6986/feature/HS6986/extend-MixtureFinder\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/df4c9ee465b16cb65e9c208e143dd9805cedea34\"\u003e\u003ccode\u003edf4c9ee\u003c/code\u003e\u003c/a\u003e update latest cmake\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/9578f2b6186aab8ba83740d41f0aa501e0193707\"\u003e\u003ccode\u003e9578f2b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/83\"\u003e#83\u003c/a\u003e from thomaskf/Ali_Taba\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/1e9303fdd449390ddf5d29a8c7cd84d783f6e457\"\u003e\u003ccode\u003e1e9303f\u003c/code\u003e\u003c/a\u003e Merge branch 'master' into feature/HS6986/extend-MixtureFinder\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/760433a85bd28583b12a807718c6f972accd33bd\"\u003e\u003ccode\u003e760433a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/29\"\u003e#29\u003c/a\u003e from IntegerLimit/mr-bayes-support-iqtree-3\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/6c6f9781f8e9b564b69c9cc344f83500d373be01\"\u003e\u003ccode\u003e6c6f978\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/73\"\u003e#73\u003c/a\u003e from StefanFlaumberg/bugfix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/28c89a58f0f96d41f3e707e7e271e3ddaa5306f1\"\u003e\u003ccode\u003e28c89a5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/75\"\u003e#75\u003c/a\u003e from Hashara/gitworkflow-memcheck\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/05983b5c641071b72ee1c8f91b658e482166e839\"\u003e\u003ccode\u003e05983b5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/76\"\u003e#76\u003c/a\u003e from magnified103/patch-1\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/46c3bf76316073d7b8267556193637e55c5d35c3\"\u003e\u003ccode\u003e46c3bf7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/88\"\u003e#88\u003c/a\u003e from trongnhanuit/alisim_bug_fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f7de1bba65819a6a77fcd220f60be75c9987b6a5\"\u003e\u003ccode\u003ef7de1bb\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/81\"\u003e#81\u003c/a\u003e from iqtree/nhan_auto_switch_pars\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/a6739a16530eec695ab85144db5c9b83abe77074...1cda77774361aac0cb152047f3d1d7c124499cea\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/329","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/329","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/329/packages"}},{"old_version":"`a6739a1`","new_version":"`760433a`","update_type":null,"path":null,"pr_created_at":"2025-09-30T04:17:01.000Z","version_change":"`a6739a1` → `760433a`","issue":{"uuid":"2872832326","node_id":"PR_kwDOLrtbes6rO_FG","number":328,"state":"open","title":"Bump iqtree3 from `a6739a1` to `760433a`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-30T04:17:01.000Z","updated_at":"2025-09-30T04:17:02.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`a6739a1`","new_version":"`760433a`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `a6739a1` to `760433a`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/760433a85bd28583b12a807718c6f972accd33bd\"\u003e\u003ccode\u003e760433a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/29\"\u003e#29\u003c/a\u003e from IntegerLimit/mr-bayes-support-iqtree-3\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/6c6f9781f8e9b564b69c9cc344f83500d373be01\"\u003e\u003ccode\u003e6c6f978\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/73\"\u003e#73\u003c/a\u003e from StefanFlaumberg/bugfix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/28c89a58f0f96d41f3e707e7e271e3ddaa5306f1\"\u003e\u003ccode\u003e28c89a5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/75\"\u003e#75\u003c/a\u003e from Hashara/gitworkflow-memcheck\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/05983b5c641071b72ee1c8f91b658e482166e839\"\u003e\u003ccode\u003e05983b5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/76\"\u003e#76\u003c/a\u003e from magnified103/patch-1\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/46c3bf76316073d7b8267556193637e55c5d35c3\"\u003e\u003ccode\u003e46c3bf7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/88\"\u003e#88\u003c/a\u003e from trongnhanuit/alisim_bug_fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f7de1bba65819a6a77fcd220f60be75c9987b6a5\"\u003e\u003ccode\u003ef7de1bb\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/81\"\u003e#81\u003c/a\u003e from iqtree/nhan_auto_switch_pars\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/df6e521a012360898f47f393889236512e0b0014\"\u003e\u003ccode\u003edf6e521\u003c/code\u003e\u003c/a\u003e Update Help Comment: Model is Always Outputted\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f462794b0afd9d847140c7445801185a567a3cd2\"\u003e\u003ccode\u003ef462794\u003c/code\u003e\u003c/a\u003e Protein: Fix Missing Endline\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/50ff3bc5370a11ae3d6060073d38a9c39600f515\"\u003e\u003ccode\u003e50ff3bc\u003c/code\u003e\u003c/a\u003e Protein: Fully Remove GTR Rate Matrix Logic\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/f1be77779a0de3036f45297d349fc1f2d036fc4a\"\u003e\u003ccode\u003ef1be777\u003c/code\u003e\u003c/a\u003e Comment: Update Fallback Model for Protein\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/a6739a16530eec695ab85144db5c9b83abe77074...760433a85bd28583b12a807718c6f972accd33bd\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/328","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/328","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/328/packages"}},{"old_version":"`7cded0c`","new_version":"`a6739a1`","update_type":null,"path":null,"pr_created_at":"2025-09-26T06:00:13.000Z","version_change":"`7cded0c` → `a6739a1`","issue":{"uuid":"3455900794","node_id":"PR_kwDOLrtbes6qoLIR","number":323,"state":"open","title":"Bump iqtree3 from `7cded0c` to `a6739a1`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":5,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-26T06:00:13.000Z","updated_at":"2025-09-27T08:01:27.782Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`7cded0c`","new_version":"`a6739a1`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `7cded0c` to `a6739a1`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/a6739a16530eec695ab85144db5c9b83abe77074\"\u003e\u003ccode\u003ea6739a1\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/93\"\u003e#93\u003c/a\u003e from thomaskf/libiqtree\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/722c99460799551977ecc9549dfe238fced563f8\"\u003e\u003ccode\u003e722c994\u003c/code\u003e\u003c/a\u003e Allow the fix the branch length as the input tree when fixing the tree for li...\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/7cded0cbc1767dab82bed39720a809f9359d7227...a6739a16530eec695ab85144db5c9b83abe77074\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/323","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/323","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/323/packages"}},{"old_version":"`993275d`","new_version":"`7cded0c`","update_type":null,"path":null,"pr_created_at":"2025-06-30T04:02:45.000Z","version_change":"`993275d` → `7cded0c`","issue":{"uuid":"2627677398","node_id":"PR_kwDOLrtbes6cnyzW","number":264,"state":"open","title":"Bump iqtree3 from `993275d` to `7cded0c`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-30T04:02:45.000Z","updated_at":"2025-06-30T04:02:45.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`993275d`","new_version":"`7cded0c`","repository_url":"https://github.com/iqtree/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/iqtree/iqtree3) from `993275d` to `7cded0c`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/7cded0cbc1767dab82bed39720a809f9359d7227\"\u003e\u003ccode\u003e7cded0c\u003c/code\u003e\u003c/a\u003e allow running CI workflow on push with every branch\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/5b2cf2468deb56a09c1e60ee5c96754bc2aa03c5\"\u003e\u003ccode\u003e5b2cf24\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/68\"\u003e#68\u003c/a\u003e from iqtree/huaiyan\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/5eb1253a15e4f1b1652b4f6a7aa4b470a904a0df\"\u003e\u003ccode\u003e5eb1253\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/71\"\u003e#71\u003c/a\u003e from thomaskf/unit_test_update\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/dcab2d0bffa41bda488202aab6ab4bfad0bf8e13\"\u003e\u003ccode\u003edcab2d0\u003c/code\u003e\u003c/a\u003e notify about auto-detect seq type for both single and partition model. mAIC d...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/48c034227fd12d0544422a189f73bc9d06ef1758\"\u003e\u003ccode\u003e48c0342\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/13\"\u003e#13\u003c/a\u003e from Hashara/unit_test_update\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/a4cff0a1f00379ba77a5fc3aa6f4f3e539cbd19f\"\u003e\u003ccode\u003ea4cff0a\u003c/code\u003e\u003c/a\u003e increase runtime threshold\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/9abfdc539c2c9c641fd7e0cfb3d1a634fe9f9563\"\u003e\u003ccode\u003e9abfdc5\u003c/code\u003e\u003c/a\u003e increase runtime threshold\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/6d12a9523e35f3151f2c770f153ccb9be40109ca\"\u003e\u003ccode\u003e6d12a95\u003c/code\u003e\u003c/a\u003e increase runtime threshold\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/8f5f22a063cae6f1f62dcb1b1fea51fbb483b2bf\"\u003e\u003ccode\u003e8f5f22a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/iqtree/iqtree3/issues/12\"\u003e#12\u003c/a\u003e from Hashara/unit_test_update\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/iqtree/iqtree3/commit/96de033d2ca661bcd3164ccd440410e4dd470c2a\"\u003e\u003ccode\u003e96de033\u003c/code\u003e\u003c/a\u003e add unit_test_update branch trigger to the workflow\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/iqtree/iqtree3/compare/993275d52e10dc026840b7028048c7e517c21e82...7cded0cbc1767dab82bed39720a809f9359d7227\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/264","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/264","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/264/packages"}},{"old_version":"`d9bc0a6`","new_version":"`ce5b6ce`","update_type":null,"path":null,"pr_created_at":"2025-06-23T04:33:24.000Z","version_change":"`d9bc0a6` → `ce5b6ce`","issue":{"uuid":"3166734741","node_id":"PR_kwDOLrtbes6blyjA","number":247,"state":"open","title":"Bump iqtree3 from `d9bc0a6` to `ce5b6ce`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":3,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-23T04:33:24.000Z","updated_at":"2025-06-23T06:11:39.334Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`d9bc0a6`","new_version":"`ce5b6ce`","repository_url":"https://github.com/thomaskf/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/thomaskf/iqtree3) from `d9bc0a6` to `ce5b6ce`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/ce5b6ceae081bffc41d433b48c7a60575211e004\"\u003e\u003ccode\u003ece5b6ce\u003c/code\u003e\u003c/a\u003e Revert \u0026quot;Move the line \u0026quot;Optimizing NNI: done...\u0026quot; to the medium verbose mode\u0026quot;\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/a39bbadbbc26ac299d621297e3eb69e6d94fa6cc\"\u003e\u003ccode\u003ea39bbad\u003c/code\u003e\u003c/a\u003e Move the line \u0026quot;Optimizing NNI: done...\u0026quot; to the medium verbose mode\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/thomaskf/iqtree3/compare/d9bc0a64e4a905b802193f418bba69a2ec1a6e54...ce5b6ceae081bffc41d433b48c7a60575211e004\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/247","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/247","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/247/packages"}},{"old_version":"`1357e36`","new_version":"`d9bc0a6`","update_type":null,"path":null,"pr_created_at":"2025-06-23T01:42:38.000Z","version_change":"`1357e36` → `d9bc0a6`","issue":{"uuid":"2610157613","node_id":"PR_kwDOLrtbes6bk9gt","number":246,"state":"open","title":"Bump iqtree3 from `1357e36` to `d9bc0a6`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-23T01:42:38.000Z","updated_at":"2025-06-23T01:42:39.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`1357e36`","new_version":"`d9bc0a6`","repository_url":"https://github.com/thomaskf/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/thomaskf/iqtree3) from `1357e36` to `d9bc0a6`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/d9bc0a64e4a905b802193f418bba69a2ec1a6e54\"\u003e\u003ccode\u003ed9bc0a6\u003c/code\u003e\u003c/a\u003e Modify the consensus tree function for iqtree library for strict consensus tree\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/thomaskf/iqtree3/compare/1357e3646cf3d51cab75f13562575cf937d67702...d9bc0a64e4a905b802193f418bba69a2ec1a6e54\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/246","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/246","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/246/packages"}},{"old_version":"`f7660f4`","new_version":"`1357e36`","update_type":null,"path":null,"pr_created_at":"2025-06-18T04:32:46.000Z","version_change":"`f7660f4` → `1357e36`","issue":{"uuid":"3155431174","node_id":"PR_kwDOLrtbes6bADSp","number":239,"state":"open","title":"Bump iqtree3 from `f7660f4` to `1357e36`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-18T04:32:46.000Z","updated_at":"2025-06-18T04:59:13.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"iqtree3","old_version":"`f7660f4`","new_version":"`1357e36`","repository_url":"https://github.com/thomaskf/iqtree3"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [iqtree3](https://github.com/thomaskf/iqtree3) from `f7660f4` to `1357e36`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/1357e3646cf3d51cab75f13562575cf937d67702\"\u003e\u003ccode\u003e1357e36\u003c/code\u003e\u003c/a\u003e Merge branch 'mixFinder_update' into libiqtree\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/fc0d98452e31baf099b936d67f3f6c25af375d43\"\u003e\u003ccode\u003efc0d984\u003c/code\u003e\u003c/a\u003e Fixed the incorrect usage of ASSERT\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/d6c1f5b5843083cf0a04bfdfa97cbe9ce22f7652\"\u003e\u003ccode\u003ed6c1f5b\u003c/code\u003e\u003c/a\u003e Added the verification on the initial likelihood value after mixtureFinder\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/0743b7ad0cde1c2c544a3ff89d41e2584cf2db96\"\u003e\u003ccode\u003e0743b7a\u003c/code\u003e\u003c/a\u003e Fixed the different RHAS parameters and branch lengths between the MixFinder ...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/thomaskf/iqtree3/commit/c2eab2f788f68db03cc0bc2208563baf2085fcba\"\u003e\u003ccode\u003ec2eab2f\u003c/code\u003e\u003c/a\u003e Remove the increase of the maximum number of iterations for mixture model\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/thomaskf/iqtree3/compare/f7660f4d53f9900c867e1be985e8c98112f6b764...1357e3646cf3d51cab75f13562575cf937d67702\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/iqtree/piqtree/pull/239","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/iqtree%2Fpiqtree/issues/239","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/239/packages"}}]}