- Will be tested by our lab memebers to fix bugs and advance features
- Will be tested by peer taxonomists
"Fun"gal "V"alidation & "I"dentification "P"ipeline
An automatic tree-based sequence identification and validation pipeline for fungal species
- Automatic tree-based identification
- Works with multigene
- Data validation algorithm implemented
See tutorial for step by step tutorial
See documentation for advanced usage
- Conda environment (See https://www.anaconda.com/products/individual for how to install conda environment)
conda create -n FunVIP python>=3.9
conda activate FunVIP
pip install FunVIP
- run
FunVIP --test Terrei --email [your email]
to check installation
- For upgrade use this command
pip install FunVIP --upgrade
conda create -n FunVIP python>=3.9
conda activate FunVIP
pip install FunVIP
conda config --add channels conda-forge
conda install -c bioconda raxml iqtree "modeltest-ng>=0.1.7" mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree
- run
FunVIP --test Terrei --email [your email]
to check installation
- For intel mac system, this method probably work, but we couldn't test it because we don't have any intel mac device. We're looking for feedbacks in intel mac
softwareupdate --install-rosetta
CONDA_SUBDIR=osx-64 conda create -n FunVIP python>=3.9
conda activate FunVIP
conda config --env --set subdir osx-64
conda install pyqt
pip install FunVIP
conda install -c bioconda raxml iqtree mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree
- run
FunVIP --test Terrei --email [your email]
to check installation
- this is for developmental steps
git clone https://github.com/Changwanseo/FunVIP.git
- Move to
~/FunVIP
conda create -n FunVIP python=3.10
conda activate FunVIP
pip install ./
- run
FunVIP --test Terrei --email [your email]
to check installation
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} --gene ITS BenA RPB2 CaM --preset fast
* See documentation for detailed usage
Section Assignment.xlsx
: Your clustering result is here. You can find which of your sequences are clustered to which sectionIdentification_result.xlsx
: Your final identification result. Shows how your sequences were assigned to species level through tree-based identificationreport.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
GPL 3.0