function sedinho () { sed -i  "s/^.*\]/>$1/g" $2;}
export -f sedinho 

##</code><code>##

LIST1=($(cat Headers.txt))
LIST2=($(find /folder/with/fasta/files/ -maxdepth 0 -name "*CDS.fasta" | sort))

parallel --xapply sedinho {1} {2} ::: ${LIST1[@]} ::: ${LIST2[@]}