FAMD

FAMD is a handy little application that helps with DNA fingerprinting studies like AFLP, RAPD, and ISSRs. Now, we all know these studies can come with their fair share of uncertainties. Whether it's noise from the technique or mistakes in scoring, things can get tricky!

Scoring Your Data

When you're working with your data, you can score it using absence/presence (0/1). This means you'll try to sort data points that you're unsure about into absences and presences. Just a heads-up: it's safer to assume they're absences rather than presences if you're feeling conservative.

Handling Uncertainties

If you want to be a bit more flexible, there's another option: (0/?/1). This lets you take a second look at your data later on and see how any ambiguous or missing information might affect your analysis.

Features of FAMD

The best part? FAMD is super easy to use! It specifically tackles missing or unclear data by offering some cool features:

• Minimum, maximum, and average (dis)similarity calculations—this helps estimate how missing data might impact your results.


• You can also explore Jaccard's, Dice, SMC similarities, NeiLi and Euclidean distances.


• The app outputs distance matrices for better clarity.


• If you've got missing data, FAMD offers resampling options too!


• You can estimate Shannon's index using bootstrapping methods.


• Create UPGMA, NJ trees along with strict and majority rule consensus trees for deeper insights.


• It even estimates R-support!


• A PCoA (principal coordinate analysis) tool comes with a 3D viewer that supports bitmap and metafile formats.


• You’ll love AMOVA for all the implemented (dis)similarity measures!


• The app allows exporting data in various formats like Nexus, Arlequin projects, hindex files, Hickory (Nexus Alleles block), GenePop, NTSYSpc, Structure files—super versatile!


• Bayesian estimation of population null allele frequency plus calculation of inter-population distances are also included!

If you're diving into DNA fingerprinting studies and want to tackle those uncertainties head-on while keeping it simple and effective, give FAMD a try!