addes some comments to improve readability

module1_2/inputData/project-buxus/Genomes.txt

@@ -7,5 +7,5 @@
 19990	Vitis	3	19
 
 # Tree in Newick Format:
-(((28620, 35405), (57266, 57268)), (19990, 54057))
-
+#(((28620, 35405), (57266, 57268)), (19990, 54057))
+(((Aquilegea_28620, Nelumbo_35405), (Tetracentron_57266, Buxus_57268)), (Vitis_19990, Amaranthus_54057))

module1_2/inputData/project-buxus/config.yaml

+# project name
+project_name: "project-buxus"
+
 # input : path to genome information file
 input_file:
   leaf_genome_info: "/Genomes.txt"
@@ -22,8 +25,9 @@ input_path: "../inputData/"
 # output path
 output_path: "../outputData/"
 
-# project name
-project_name: "project-buxus"
+
+## Global parameters
+
 
 # range of percent identity of ortholog pairs
 min_cutoff_weight: 65

module1_2/inputData/project-monocots/Genomes.txt

@@ -8,6 +8,7 @@
 #treenode_number	window_size	genome_number	gf_number
 # Tree in Newick Format:
 (((51364, 54711), 51051), ((25734, 33018), 33908))
+#(((Spirodela_51364, Acorus_54711), Dioscorea_51051), ((Ananas_25734, Elaeis_33018), Asparagus_33908))
 #51364	54711	25734,33018,33908,51051
 #51051	51364,54711	25734,33018,33908
 #33908	25734,33018	51051,51364,54711

module1_2/inputData/project-monocots/config.yaml

+# project name
+project_name: "project-monocots"
+
 # input : path to genome information file
 input_file:
-  leaf_genome_info: "/test2.txt"
+  leaf_genome_info: "/Genomes.txt"
   synteny_file_name: ".CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt"
   synteny_file_path: "/"
   jar_path: "."
@@ -22,8 +25,8 @@ input_path: "../inputData/"
 # output path
 output_path: "../outputData/"
 
-# project name
-project_name: "project-monocots"
+
+## Global parameters
 
 # range of percent identity of ortholog pairs
 min_cutoff_weight: 65