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  1. or download this
    function sedinho () { sed -i  "s/^.*\]/>$1/g" $2;}
export -f sedinho
  2. or download this
    LIST1=($(cat Headers.txt))
LIST2=($(find /folder/with/fasta/files/ -maxdepth 0 -name "*CDS.fasta"
+ | sort))

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