Phran is a perl script that uses Phred to process a set of ab1 sequence chromatograms and add the good-quality sequences to an existing alignment.
Phran depends on two external programs. First, it wraps around phred to determine the quality of the base calls in the ab1 files. Second, it uses MAFFT align good-quality sequences with the reference alignment. So you will have to download and install these programs before you can use PMT.
I've only used the program on Linux and Mac OS X but if you're computer-savvy you should be able to get it to run on Windows, too.