improved notebook

module1_2/inputData/project-buxus/Genomes.txt

-genomeID	genomeName	ancestor	numChr	gff
+#genomeID	genomeName	ancestor	numChr	gff
 28620	Aquilegea	1	7	
 35405	Nelumbo	1	8
 57266	Tetracentron	2	19

module1_2/inputData/project-monocots/config.yaml

 # input : path to genome information file
 input_file:
-  leaf_genome_info: "/Genomes.txt"
+  leaf_genome_info: "/test2.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: "./"

module1_2/inputData/project-monocots/test2.txt

-genomeID	genomeName	ancestor	numChr	gff
-28620	Aquilegea	1	7	
-35405	Nelumbo	1	8
-57266	Tetracentron	2	19
-57268	Buxus	2	14
-54057	Amaranthus	3	16
-19990	Vitis	3	19
-
-# Tree in Newick Format:
-((28620, 35405), (57266, 57268), (19990, 54057))
-