those suffixes are meaningless: show us the xml and the aln please.

There are various multiple alignment formats (http://www.bioperl.org/wiki/Multiple_alignment_formats) and .aln or .xml aren't one of those. Refer the link to see what they really are and then we can help.

At a guess you probably mean the Clustal alignment format for '.aln', which is handled by a wide range for alignment editors and reformatting tools, however for '.xml' you could be referring to any of a number of XML formats (for examples see http://www.ebi.ac.uk/Tools/webservices/tutorials/aa_xml_formats). The XML formats generally are associated with specific applications, so it may be that they have some option to convert into Clustal format, or to another commonly used format (e.g. MSF, fasta or PHYLIP) which can be handled by commonly available tools.

closing because no longer relevant and insufficient information given.