Name		Name	Last commit message	Last commit date
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.gitignore		.gitignore
README.md		README.md
extract-convex-subtrees.py		extract-convex-subtrees.py
fetch-phylota-trees.sh		fetch-phylota-trees.sh
fetch-taxonomy.sh		fetch-taxonomy.sh
filter-trees.py		filter-trees.py
make-taxonomy-graph.py		make-taxonomy-graph.py

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experimental code for extracting 'convex subtrees' (rooted subtrees corresponding to a monophyletic taxon) from unrooted phylota trees

requires latest git version of ivy

fetch the NCBI taxonomy

sh fetch-taxonomy.sh

make a taxonomy graph

python make-taxonomy-graph.py

fetch phylota trees (pb184)

sh fetch-phylota-trees.sh

filter out problematic trees (can't be read due to newick-unfriendly labels)

python filter-trees.py

extract convex subtrees from readable phylota trees

python extract-convex-subtrees.py

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