#! /usr/bin/env bash
mkdir -p treeshrink
for i in trimed_nal/*.trimed.fa; do
    j=$(basename "$i")
    mkdir -p treeshrink/"${j/.trimed.fa/}"
    cd treeshrink/"${j/.trimed.fa/}" || exit 1
    ln -s ../../fasttree/"${j/.trimed.fa/.tree}" input.tree
    ln -s ../../"$i" input.fasta
    cd ../../
done
run_treeshrink.py -i treeshrink/ -t input.tree -a input.fasta > treeshrink.log