Add commands to run all steps of example

Examples/commands/2-Pangenome.sh

+genomeAPCAT pangenome -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -n EXAMPLE4 -d Examples/1-res-Annotate/Proteins -i 0.8 -o Examples/2-res-pangenome
+

Examples/commands/3-Corepers.sh

+genomeAPCAT corepers -p Examples/2-res-pangenome/PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst    

Examples/commands/4-Align.sh

+genomeAPCAT align -c Examples/3-coregenome/PersGenome_PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst_1.lst -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -d Examples/1-res-Annotate/ -o Examples/4-Algn -n EXAMPLE4

Examples/commands/5-Tree.sh

+genomeAPCAT tree -a Examples/4-Algn/Phylo-EXAMPLE4/EXAMPLE4.grp.aln