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@rneher rneher released this 31 Jul 09:48
· 36 commits to master since this release
v0.11.0
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Learn about vigilant mode.

Feature: Better clock-filtering

Previously, only a crude analysis of whether the divergence of tips roughly follows a linear trend was implemented. Tips that deviated too much from that regression line were flagged as outliers and this threshold was parameterized as number of interquartile distances of the distribution of residuals n_iqd. This filter is not very sensitive and often misses misdated tips that severely distort the tree but still fall within the distribution of root-to-tip distances at that time. To overcome this, we implemented a novel filtering method that fits a simple gaussian model of divergence accumulation. Information on outliers is saved in a pandas DataFrame self.outliers of TreeTime and written to file as a tsv file when running treetime as command line tool.

Other fixes

  • error when rate estimate is negative during the rate susceptibility calculation. Give hint in error message to specify the rate and its uncertainty explicitly.
  • Fix bug issue #250 introduced in 0.10.0 where treetime fails in absence of an alignment when trying to create an auspice json file. PR #251
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