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Published 20 hours ago • verified publisher icon Ensembl

Use tree refinement and constraint topology in species tree pipeline

Open ens-sb opened this issue 9 months ago • 1 comments

Description

There is a need for specifying a topology constraint in the pipeline in order to allow adding new genomes to an existing topology while keeping it fixed.

Related JIRA tickets:

  • ENSCOMPARASW-7374

Overview of changes

Change 1

Using the astral tree as starting topology instead of constraint in the protein branch length calculation step.

Change 2

Added option to specify constraining topology as a newick file.

Testing

The pipeline was tested on the vertebrates 112 division. The run finished in 5 hours.

For code reviewers: code review SOP

ens-sb avatar May 10 '24 07:05 ens-sb