At first you may to check chromatogram peaks visually by trace viewers ( in such way you can estimate heght of each peak and absence of doble signal). After this you may use some programs as SeqAssem, Staden package, PAUP, TotalLab or another ones to estimate chromatograms' quality automatically by some mathematical algorithms. Nowadays a lot of such software accessible to use for this search, some part of these is freeware. List of such soft also depend on what operation system do you use and specific singularity of analysis in every case. The way, what will be potentially the best for you depends on quantity of sequences, their lenth, variability, time for analysis and some other factors.
May I add that if you use an ABI sequencer normally there is a CD with seqscape and seqscanner software on it, the scanner is pretty good for evaluating all kinds of aspects of your sequences (the sequencers normally come with licences so it should be possible to use if this does not work email me and I'll tell you how to solve this).The Geneious software package also does a good job in my opinion in helping to determine the overall quality of your sequences.
Further quality and usefullness of sequences depends on a few things (bakcground noise, double signal, peak spacing), but provided a peak is clear in your chromatogram (not too much background noise or a double signal) a Phred score of 20-25 is absolutely minimum. I generally discard sequences if the average value, or a large stretch, is below 25.
Calculate the Chromatographic performance parameters using the data of 6 repetitive injections of system suitability solution (tR, k', USP-Resolution, Alpha-, USP-N, t tailing or peak asymmetry, peak width at 0.5% height, and RSD for each parameters)
Quick and dirt experiment is usually tried first to test the separation and to decide if your system is suitable or need adjustments. Peaks should completely separated (if using any non-specific detector. i.e. not MS) R>1.3; Peak width around 0.8 min, more peak width is acceptable for Rt>20 min, it is not general rule.
The freely available BioEdit software may solve your purpose, its a very good software where you can study as well s edit all the parameters as per your desire
I use vector nti. Find it convenient. Unfortunately it's no longer free. A straight forward thing would be to ensure good resolution of the peaks. I find looking at the trace allows a good supplementary analysis. Sometimes, the software may not give accurate base calling especially in stretches.
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