AssembLIGN is not a very good contig alignment program (tho MacVector is
very good at other things, particularly primer design). Both Sequencher and
Phrap/Phred would have no problem assembling your data. If you can access
Phrap/Phred for $500 per year this is the cheaper way to go since Sequencher
costs about $3000. However, double check before making any decision that
the Licor format of chromatograms can be read by the software since most
packages are geared to ABI chromatograms. Since you are currently using
AssembLIGN you must have to assemble only the text files and not the
chromatograms. This makes your life doubly difficult due to the fact that
you have to export the files as text files, assemble them and then have to
edit the contigs without the help of examining the chromatograms in the
contigs. Both Sequencher and Phred/Phrap don't have this limitation.
Hope this is useful.