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Update README.md
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blinard-BIOINFO authored Jul 17, 2024
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Expand Up @@ -23,6 +23,30 @@ conda config --set channel_priority strict
mamba install ipk epik
```

Rapid test:
```
# get some test alignment and tree
wget https://github.com/phylo42/IPK/blob/main/tests/data/D652/reference.fasta
wget https://github.com/phylo42/IPK/blob/main/tests/data/D652/tree.rooted.newick
# activate conda environment
conda activate epik
# build database with IPK : using 1 CPU and default phylogenetic model parameters
# a better approach would be to use appropriate parameters, see documentation
ipk.py build --refalign reference.fasta --reftree tree.rooted.newick --states nucl --workdir . --model GTR
# place with EPIK
epik.py place -i DB.ipk -s nucl -o . reference.fasta
# jplace results
cat placements_reference.fasta.jplace
# you can do post-analyses with the excellent 'gappa' package
# (available in bioconda too, see https://github.com/lczech/gappa)
```


## Installation via compilation

### Prerequisites
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