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Clean-up of rerooting mechanisms
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@rneher rneher released this 16 Feb 05:35
· 560 commits to master since this release
v0.5.4
35141ef

This release consolidates the rerooting mechanisms into min_dev, least-squares and oldest. In addition, the command-line tools now accept lists of nodes or a single node as outgroup. Whether covariation due to shared ancestry is accounted for during rerooting can be controlled by the additional flag --covariation. Other changes include:

  • tip-slack, variance associated with tips in covariance-aware regression, is now exposed to the command line as --tip-slack
  • by default, commands don't account for shared ancestry covariance as this was causing issues in densely sampled trees.
  • updated comments and help texts surrounding rerooting. Previous rerooting mechanisms still work but will print a deprecation message.
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