New to barcoding - need help with analysis

My colleage and I are new to DNA barcoding and we need help with data analysis.  We have sequenced matK, rbcL, and trnH-psbA in six tree species, and have used this data to determine the presence of a barcode gap.  But now we are stuck!  We are unsure how to proceed - analyses to perform, including statistical analyses.  Any help would be greatly appreciated!

Thanks in advance!