FAMD - Fingerprint Analysis with Missing Data Software

Fingerprint Analysis with Missing Data 1.3 Software

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FAMD (here)

NEW [26/08/2014]. GbsPro for getting NGS data into FAMD is now available.

[18/10/2013]. FAMD 1.31 is available for download here.

[06/06/2008]. Since I am no longer at the University of Vienna, I have moved the FAMD web site from the University of Vienna (previous location was http://homepage.univie.ac.at/philipp.maria.schlueter/famd.html) to www.famd.me.uk, which I intend to keep as a stable URL.

FAMD is a Win32 program. It can be run under linux if you are using wine.

Why FAMD?

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:

minimum/ maximum/ average (dis)similarity calculation allowing the estimation of the extent to which missing data may impact on the analysis.
Jaccard's, Dice, SMC similarities, NeiLi and Euclidean distances
output and import of distance matrices
missing data resampling
estimation of Shannon's index by bootstrapping, including resampling at a specified number of individuals.
UPGMA, NJ, strict and majority rule consensus trees
estimation of R-support
PCoA (principal coordinate analysis) and 3D viewer with bitmap and metafile support
AMOVA for all implemented (dis)similarity measures
export of data to a number of formats such as Nexus, Arlequin project, hindex, Hickory (Nexus Alleles block), GenePop, NTSYSpc, Structure, hindex, AFLPDat, AFLPop, dfdist, BayeScan, etc.
import of distance matrices and import of count data (e.g. sequenced tags from next-generation sequencing [NGS]-based methods like GBS or RAD-Seq).
Bayesian estimation of population null allele frequency and calculation of inter-population distances
Maximum likelihood hybrid index calculation.
Maximum likelihood population (re)allocation.
Plotting functionality for [selected] results (based on R).

[26/08/2014] To generate FAMD input files and count tables from NGS-based files (FASTQ), you may want to use GbsPro (download here).

More detailed descriptions of what FAMD actually does can be found in the accompanying help file/manual. The paper dealing with FAMD, and the effects of missing data on data analysis, has been published:

Schlüter, P. M. & Harris, S. A., 2006, Analysis of multilocus fingerprinting data sets containing missing data. Mol. Ecol. Notes. 6: 569-572. [Abstract] [Papers citing FAMD]

[18/10/2013] FAMD 1.31 is now available for download. By downloading FAMD you agree to the legal disclaimer below. The included help file has now been updated.

Legal disclaimer
FAMD (c) Copyright 2002-2013 Philipp M Schlüter.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, whether expressed or implied; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. The author (PMS) will not be liable for any special, incidental, consequential, indirect or similar damages due to loss of data or any other reason, even if he or an agent of his has been advised of the possibility of such damages. In no event shall the author be liable for any damages, regardless of the form of the claim. The person using the software bears all risk as to the quality and performance of the software.

As is always the case with software, FAMD is being improved and newer versions will be put here from time to time. The program is provided as-is. The program was tested thoroughly under realistic situations and appeared to behave well during these tests. However, while I strive to correct any bugs I come across, there are bound to be some bugs hiding somewhere. Of course I cannot accept any responsibility for stupidities you may want to do using this program and hence I cannot be held responsible for any damage you do to your system (or data) by using it.

Installation: Simply unzip the downloaded file and place the two files contained therein in the same directory (folder) and start the file famd.exe (or just "famd" if extensions aren't shown on your computer) by clicking on it. In order to view the help file, you must have Acrobat Reader installed, or any other program that can display pdf files. FAMD does not do any such things as writing anything to your Windows registry. Hence, to remove FAMD, you can simply delete it.

Download sample data set. This is the raw data set used in the Mol. Ecol. Notes paper. Also included are sample output files generated from that data set.

Please. If you are using FAMD and would like to be informed about the latest version, changes, bug-fixes, etc., then please do send me an e-mail. Thanks.
You can reach me at firstname(dot)lastname[at]systbot(dot)uzh(dot)ch (spelling my last name "schlueter").

If you have any specific problems or questions with FAMD, then please let me know. This also applies if you wish to see specific changes to the source code.

Known issues and bugs can be found here.

If for one or the other reason, you would like to use an older version of FAMD, they are available here.