Codes and commands for Ata genome analysis
#Biased expression between LF and MF:
1.Transcriptomes.txt
#Subgenome fractionation tests between LF and MF:
2.SubgenomeFractionation.txt
#Biased TE distribution between LF and MF:
3.TEdivergenceBtwLF_MF.txt
#Synteny retention rate variation among monocots, when compared to 3 outgroup species:
4.Synteny_retention_in_monocots.txt
#Copy number difference tests of ortholog groups between monocots and dicots:
5.OG_copyNum_compare.txt
#Perl script for calculating CIP and CALP in ancestral karyotype reconstruction
6.CIP_CALP.pl
#workflow from one-to-one conserved ortholog (protogenes), syntenic blocks (SBs) to protochromosomes (CARs)
7.Protogenes_SBs_CARs.txt