update commands for pll examples

examples/libpll_examples/fake_example/command.txt

-Run the following from the root path of Treerecs:
-build/bin/Treerecs -g examples/libpll_examples/fake_example/gene_tree.txt -s examples/libpll_examples/fake_example/species_tree.txt -t 0.5 -a examples/libpll_examples/fake_example/alignments.txt  --threshold all --ale-evaluation
-
+treerecs -g gene_tree.txt -s species_tree.txt -t 0.5 -a alignments.txt  --threshold all--ale-evaluation

examples/libpll_examples/real_example/command.txt

-bin/Treerecs -g examples/libpll_examples/real_example/gene_tree_HBG011000.newick -s examples/libpll_examples/real_example/speciesTree.newick -a examples/libpll_examples/real_example/alignment.txt -t 0.5 --ale-evaluation -T 7 -S examples/libpll_examples/real_example/HBG011000.map
+treerecs -g gene_tree_HBG011000.newick -s speciesTree.newick -a alignment.txt -t 0.5 --ale-evaluation -S HBG011000.map