* if your alignment file is in giza format:

perl  orderA3as_alignref-version.pl -cs reference_sentences_source -ct
       reference_sentences_target< src2trg_giza_file >src2trg_giza_reference_file

* if your alignment file in not in giza format you may write an equivalent script 
or use the Lingua::AlignmentSet toolkit (it is not as efficient as it must load 
the links in a perl structure and then read from this structure):

see a code sample doing:

perl orderAlSetAsBilCorpus.pl -man