An efficient toolkit for constructing and processing taxonomic trees (abundance calculations, reading count statistics, etc.).
Project description
living-tree-toolkit
An efficient toolkit for processing taxonomic trees (abundance calculations, reads count statistics, etc.) and generating taxonomic trees using lineages data retrieved from the NCBI taxonomy database.
Use treelib
API to achieve rapid construction of complex trees and ete3 toolkit
API to retrieve data from NCBI taxonomy database.
This project is a sub-project of the ONN4MDM project, if you use it for academic purposes, please cite us.
Update
- 2020/03/27:
- start finalizing project framework and release initial version.
- 2020/04/14:
- Api update
update_value
andget_matrix
- New method
get_top_down_ids
,get_bottom_up_ids
,get_ids_by_level
andget_paths_to_level
- Execution efficiency are improved significantly
- Api update
Documentation
For Installation, examples and API references, see https://living-tree-toolkit.readthedocs.io/en/latest/
Maintainer
Name | Organization | |
---|---|---|
Hui Chong | ch37915405887@gmail.com | Research Assistant, School of Life Science and Technology, Huazhong University of Science & Technology |
Project details
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