FAMD (Fingerprint Analysis with Missing Data) can analyze DNA sequences with this tool. DNA fingerprinting (AFLP, RAPD, ISSRs, etc.) studies will inherently bring uncertainties with them, whether that be noise associated with the technique, or errors made in scoring, etc.

This program was originally written for analysis of RAPD, AFLP or other dominant (binary) fingerprint data, especially for data sets that contain ambiguous or missing data, so that the impact that missing data may have on the analysis can be better evaluated. The second intention was to provide a means to easily calculate the variance associated with Shannon's index. However, as outlined in this manual, since its beginnings FAMD has accumulated a number of additional features.

DNA fingerprinting (AFLP, RAPD, ISSRs, etc.) studies will inherently bring uncertainties with them, whether that be noise associated with the technique, or errors made in scoring, etc..

You can score your data using absence/presence (0/1). This means that you will attempt to partition data points about which you are unsure into absences and presences (to be conservative, probably absences rather than presences). Alternatively, you can allow for uncertainties: (0/?/1). This enables you to later have a second look at your data and ask what impact this ambiguous or missing data may have on your analysis.

Fingerprint Analysis with Missing Data (FAMD) is a little tool to help you doing that. Specifically addressing missing (or ambiguous) data, FAMD (1.1 and later) implement the following:
1. minimum/ maximum/ average (dis)similarity calculation allowing the estimation of the extent to which missing data may impact on the analysis.
2. Jaccard's, Dice, SMC similarities, NeiLi and Euclidean distances
3. output of distance matrices
4. missing data resampling
5. estimation of Shannon's index by bootstrapping.
6. UPGMA, NJ, strict and majority rule consensus trees
7. estimation of R-support
8. PCoA (principal coordinate analysis) and 3D viewer with bitmap and metafile support
9. AMOVA for all implemented (dis)similarity measures
10. export of data to a number of formats such as Nexus, Arlequin project, hindex, Hickory (Nexus Alleles block), GenePop, NTSYSpc, Structure, hindex.
11. Bayesian estimation of population null allele frequency and calculation of inter-population distances

The license of this software is Freeware, you can free download and free use this calculator software.