diff --git a/README.md b/README.md index 2366d25..2e2d50f 100644 --- a/README.md +++ b/README.md @@ -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