fix conflict and merge

module1_2/inputData/project-buxus-tree2/57268_57268.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+57268_57268.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/Genomes.txt

+#genomeID	genomeName	ancestor	numChr
+54057	Amaranthus	1	16
+19990	Vitis	1	19
+57266	Tetracentron	2	19
+57268	Buxus	3	14
+28620	Aquilegea	4	7	
+35405	Nelumbo	4	8

module1_2/inputData/project-buxus-tree2/karyotype/karyotype_19990_Vitis.txt

+karyotype_19990_Vitis.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/karyotype/karyotype_28620_Aquilegea.txt

+karyotype_28620_Aquilegea.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/karyotype/karyotype_35405_Nelumbo.txt

+karyotype_35405_Nelumbo.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/karyotype/karyotype_54057_Amaranthus.txt

+karyotype_54057_Amaranthus.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/karyotype/karyotype_57266_Tetracentron.txt

+karyotype_57266_Tetracentron.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/karyotype/karyotype_57268_Buxus.txt

+karyotype_57268_Buxus.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree2/phyloTree.txt

+# Tree in Newick Format:
+((((Vitis_19990, Amaranthus_54057), Tetracentron_57266), Buxus_57268), (Aquilegea_28620, Nelumbo_35405))
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/19990_19990.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+19990_19990.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/19990_28620.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+19990_28620.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/19990_35405.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+19990_35405.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/19990_54057.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+19990_54057.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/19990_57266.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+19990_57266.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/19990_57268.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+19990_57268.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/28620_28620.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+28620_28620.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/28620_35405.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+28620_35405.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/28620_54057.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+28620_54057.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/28620_57266.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+28620_57266.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file

module1_2/inputData/project-buxus-tree3/28620_57268.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt

+28620_57268.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.gcoords.ks.txt
\ No newline at end of file