An automatic tree-based sequence identification and validation pipeline for fungal (or maybe other) species
- Automatic tree-based identification
- Works with multiple genetic marker
- Database sequence validation algorithm implemented
Bug reports are always welcomed
IMPORTANT NOTICE: The python dependency for Linux platform has changed from 3.12 to 3.11 for TCS inclusion. Please remake conda environment for FunVIP 0.3.25 update
- See Documentation for advanced usage !
- Conda or Mamba environment
* See here for how to install conda environment
* Recently, Mamba is a lot faster than conda. See here to how to install mamba environment
FunVIP --db {Your database file} --query {Your query file} --email {Your email} --gene {Your genes} --preset {fast or accurate}
FunVIP --db Penicillium.xlsx --query Query.xlsx --email {Your email} --thread 8 --gene ITS BenA RPB2 CaM --preset fast
* See documentation for detailed usage
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Section Assignment.xlsx: Your clustering result is here. You can find which of your sequences are clustered to which section -
Identification_result.xlsx: Your final identification result. Shows how your sequences were assigned to species level through tree-based identification -
report.xlsx: overall statistics about the tree. If your find taxon ends with numbers, these taxon are found to be paraphyletic, so should be checked -
/Tree/{section}_{gene}.svg: Final collapsed tree in svg format. Can be edited in vector graphics programs, or in powerpoint (by ungroup) -
/Tree/{section}_{gene}_original.svg: Uncollapsed tree for inspection -
Example output tree of FunVIP
Beta release part 1 (2023 Feburary ~ As paper published, ver 0.3) Will be tested by our lab memebers to fix bugs and advance featuresFunVIP article is currently accepted. Will be published soon.- Beta release part 2 (As paper published ~ When pipeline gets stabled, ver 0.4) Will be tested by peer taxonomists
- Stable release (ver 1.0)