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Name	Modified	Size	InfoDownloads / Week
2.0.0	2013-03-23		4
1.2.3	2013-03-23		0
README.md	2013-03-23	6.6 kB	0
FRANz.pdf	2013-03-23	57.2 kB	1
Totals: 4 Items		63.8 kB	5

FRANz 2.0.0

A pedigree (family tree) reconstruction tool for natural populations.

Key Features:

Allele frequency analyses:
- Heterozygosities
- Polymorphic Information Content (PIC)
- Exact Hardy Weinberg Test
- Test for Null Alleles
Exclusion probabilities: Estimate the power of your marker suite.
FRANz is flexible, you CAN (but don't have to!) incorporate available prior knowledge:
- Known sub-pedigrees (e.g. mother-offspring arcs) or fullsib groups
- The sex and years of birth and death of individuals
- Sampling locations (pairwise distances or coordinates)
- Sampling rate (number of unsampled males and females)

Most other tools assume that you know all or most of these.

User friendly: FRANz uses this prior knowledge to generate the lists of candidate parents internally. Once you have your data in a FRANz input file, you are almost done. A GUI for input file generation is available on our website.
Can handle data with typing errors and missing alleles.
Estimation of the number of unsampled candidate mothers and fathers.
FRANz is fast: It was written for data sets with thousands of individuals. It supports modern CPUs with multiple cores.
Available for Windows, Mac and Linux.
Open Source: Obtain FRANz under the GPL Version 3.

Currently NOT supported

This is not exactly a TODO list, these are some features we might implement if there is a demand. Please don't hestitate to contact us if you need one of these features:

support for haplo-diploid species
support for dominant markers
We also don't support what Sheehan and Egeland (doi 10.1111/j.1469-1809.2006.00345.x) call "soft prior information". One example here would be an age dependent probability for sexual reproduction, for example with something like

--femrepro 2:8 --femreproprob 1,2,3,4,3,2,1

we could say that the reproductive potential of a three year old female is twice the one of two year old females.

Installation

Source Package

If possible, try to compile FRANz. Supporting the different versions of the major operating systems is difficult, but the source code should always work. If you have trouble compiling the code on Linux or Mac, please contact us. Download the latest stable source code from SourceForge.net:

http://sourceforge.net/projects/franzpedigree/files/

Alternatively, get the newest code from github:

https://github.com/lima1/franzpedigree/tarball/master

Then unzip:

tar xvfz lima1-franzpedigree-30eaf35.tar.gz
cd lima1-franzpedigree-30eaf35

Then compile:

autoreconf (only necessary if you use the latest code from github)
./configure 
make check  (optional, may take a while)
make install

For multicore CPUs (requires GCC >=4.2 or ICC).

./configure --enable-openmp
make check (optional)
make install

Mac OS X

For Leopard or newer, you can either download the installer or you can compile the source package (this works with older Mac OS X Versions as well).

To compile the source package, you need the Apple Developer Tools. To enable OpenMP, you have to compile FRANz with gcc-4.2 (or newer) or Intel's ICC. GCC 4.2 is available on Leopard:

./configure --enable-openmp CC=gcc-4.2
make check (optional)
make install

Make sure that you use gcc or icc for OpenMP; on newer Mac versions, you have to install the command line tools in XCode 4.3 or newer.

On Tiger if you don't want to install a recent compiler (e.g. from finkproject.org):

./configure
make check (optional)
make install

Windows

If you want to install FRANz on Windows, you can use the installer available from our website. Currently, only the single CPU version is available for Windows. Linux and Mac are still the recommended platforms.

To compile the source package, you will need something like Cygwin (this should give you the multi-core Version) or MinGW (there are experimental releases with OpenMP support). Make sure that FRANz is compiled with -DWIN32. Otherwise at least the progressbar will not work.

Additional configure Flags

--enable-openmp      OpenMP support
--enable-debug       Enables debug code and compiles with -g -O0
--enable-assertions  Enables assertions. Warning: will make the program
                     really slow

Tutorial

Once you have your data in the input format, analyzing it should be easy. There are some Perl scripts in extras/input to convert Excel (saved as CSV-file) or migrate data. There is also an user friendly CSV to FRANz converter available on the FRANz website.

Also check the manpage

man FRANz

Troubleshooting

Most of the problems are related to wrongly formatted input files. If you get a segmentation fault, please if possible try to re-compile with --enable-debug. Then start FRANz in the GNU debugger:

$ gdb lima1-franzpedigree-30eaf35/scr/FRANz

Then run the program with the same set of paramaters:

GNU gdb 6.3.50-20050815 (Apple version gdb-1515) (Sat Jan 15 08:33:48 UTC
2011)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-apple-darwin"...Reading symbols for shared
libraries .. done

(gdb) run input.dat --femrepro 1:10 --malerepro 1:10 --N 10

After the segmentation fault, type backtrace and send us the output with your bugreport:

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
0x00007fff86bddc00 in strlen ()
(gdb) backtrace

Feedback

Any comments, questions, critics or suggestions are gratefully received. So please don't hesitate to contact us! We would be happy to help. Your feedback will help us improving this software.

markus@bioinf.uni-leipzig.de