Multiple clones Sanger sequencing analysis
I haven't personally used it but seqtrace seems to be targeted for this purpose. It seems to be able to do alignments and facilitates multiple trace file analysis.
I worry a little bit about not visually inspecting trace files for sequencing of clones, but I may be a relative dinosaur (about sanger at least).
Here is the abstract:

Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace. googlecode.com/.© 2012 ABRF.