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Add thorney beast support in Beauti#1211

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jtmccr1 wants to merge 31 commits intomasterbeast-dev/beast-mcmc:masterfrom beauti-tbbeast-dev/beast-mcmc:beauti-tbCopy head branch name to clipboard

+7,220-188

Commits

Commits on Jul 10, 2024

• initial look at beauti

  jtmccr1

  committed
  a392217

• git ignore for vscode

  jtmccr1

  committed
  d368683

• unhide thorney options for dev work

  jtmccr1

  committed
  236324d

Commits on Jul 11, 2024

• removes treedatapartition from sites and substitution model

  jtmccr1

  committed
  0637872

• adds thorney operators

  jtmccr1

  committed
  ed3bc28

• Adds initial tree

  jtmccr1

  committed
  b22eb1f

• adds likelihood block

  jtmccr1

  committed
  183d17e

Commits on Jul 12, 2024

• fixes bug in treemodel idref

  jtmccr1

  committed
  d2d768f

• operator work

  jtmccr1

  committed
  b952961

• thorney beast uses bft-intervals nows

  jtmccr1

  committed
  3661e10

• removes unneeded components

  jtmccr1

  committed
  77fb51d

• trying out clock models with tb

  jtmccr1

  committed
  0fe7bfb

• proxy parameters so we can use usual node height operators

  jtmccr1

  committed
  7de04b3

• adds node height proxies and standard operators

  jtmccr1

  committed
  b11d856

• fixes bug in rate covariance that failed if parent was null

  jtmccr1

  committed
  062fc43

Commits on Jul 27, 2024

• Merge remote-tracking branch 'origin/master' into every-rose

  jtmccr1

  committed
  ad814b2

• adds beauti generated example for 1K SARS2

  jtmccr1

  committed
  8128df3

Commits on Aug 7, 2024

• removing comments

  jtmccr1

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  ad4147c

Commits on Oct 2, 2024

• subtree slide works with bft (no trait swaps through)

  jtmccr1

  committed
  344a22e

Commits on Oct 21, 2024

• forgot treemodel edits in constraints

  jtmccr1

  committed
  b42c751

• capitalization in rootheightproxy

  jtmccr1

  committed
  a304f9b

• adds bft to beauti jar

  jtmccr1

  committed
  6fed2cb

Commits on Nov 19, 2024

• Merge remote-tracking branch 'origin/master' into every-rose

  jtmccr1

  committed
  f9bb47c

• resolving AR conversations

  jtmccr1

  committed
  e6d89aa

• updates bft and constrained tree to default xml

  jtmccr1

  committed
  8aed018

• removes duplication of empirical trees from tree panel

  jtmccr1

  committed
  f80a82b

• adds warning for clock models without TB gradients

  jtmccr1

  committed
  e8a0c43

• updating constrained tree xml in unit tests

  jtmccr1

  committed
  7d2bd2a

Commits on Dec 18, 2024

• Revert "thorney beast uses bft-intervals nows"

  Show description for 8226901
  jtmccr1

  committed
  8226901

• Merge remote-tracking branch 'origin/master' into beauti-thorne

  jtmccr1

  committed
  d3bd9e6

• reverting copyright sign

  jtmccr1

  authored
  41c40e7