Add commands for example

Examples/commands/1-Annotate.sh

-# With prokka
-PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prokka -l Examples/input_files/list_genomes.lst -n EXAM --l90 3 --nbcont 10
-
-
-# With prodigal
-PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prodigal -l Examples/input_files/list_genomes.lst -n EXAM  --l90 3 --prodigal --small 

Examples/commands/2-Annotate.sh

+# Only QC
+PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -r Examples/2-res-QC -Q
+
+# With prokka
+PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
+
+
+# With prodigal
+PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prodigal -l Examples/input_files/list_genomes.lst -n GENO  --l90 3 --prodigal --small 

Examples/commands/2-Pangenome.sh

-PanACoTA 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

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

Examples/commands/3-Pangenome.sh

+PanACoTA pangenome -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3 -d Examples/2-res-prokka/Proteins -i 0.8 -o Examples/3-pangenome
+

Examples/commands/4-Align.sh

-PanACoTA 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/4-Corepers.sh

+# core genome
+PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers
+
+# strict persistent at 95%
+PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers -t 0.95

Examples/commands/5-Corepers.sh

+PanACoTA align -c Examples/4-corepers/PersGenome_<pangenome-filename>_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align

Examples/commands/5-Tree.sh

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

Examples/commands/6-Tree.sh

+PanACoTA tree -a Examples/5-align/Phylo-GENO3_1/GENO3_1.grp.aln -o Examples/6-tree
\ No newline at end of file