#! /bin/bash

aln_fn=$1
tree_fn=$2

cp $aln_fn  "input.fasta"
cp $tree_fn "input.tre"

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

python $DIR/tree_shrink/treeshrink.py -i input.tre
cp input_treeshrink/input_shrunk_0.05.tre "shrunk_0.05.tre"

python $DIR/utils/sample_from_subtree.py input.fasta shrunk_0.05.tre shrunk_0.05.fasta 
