Expose two additional options of TreeTime in augur refine by rneher · Pull Request #1203 · nextstrain/augur (original) (raw)

flags in augur refine.

• --stochastic-resolve was added in TreeTime 0.9.6 (hence update to dependencies in setup.py) and uses a different algorithm for polytomy resolution in TreeTime. Instead of pulling successively merging the two branches the increase the likelihood most, this mode generates random coalescent trees. This is faster and leads to more typical resolutions.
• --max-iter controls the number of iterations TreeTime uses to infer time trees. This was previously hard coded to 2.

marked this pull request as draft

April 18, 2023 20:34

rneher marked this pull request as ready for review

April 23, 2023 19:29

rneher deleted the feat/stochastic-polytomy-resolution branch

April 26, 2023 11:51

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