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1. etetoolkit/ete etetoolkit/ete Public

   Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the …

   Python 854 222

2. eggnogdb/eggnog-mapper eggnogdb/eggnog-mapper Public

   Fast genome-wide functional annotation through orthology assignment

   Python 666 112

3. etetoolkit/cookbook etetoolkit/cookbook Public

   HTML 19 9

4. eggnogdb/emapper-benchmark eggnogdb/emapper-benchmark Public

   Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.

   Jupyter Notebook 20 4

5. etetoolkit/treematcher etetoolkit/treematcher Public

   Search flexible patterns within tree structures using regular expression like syntax.

   Python 10 13

6. test_branch_support_after_tree_rerooting test_branch_support_after_tree_rerooting Public

   Additional test cases of branch support rearrangements after tree re-rooting inspired by http://biorxiv.org/content/early/2015/12/25/035360 (APE, dendropy, biopython, ete3, newick-utilities, bioperl)

   R 2 1