Enabling Research in Evolutionary Biology
AnA-FiTS is an efficient tool for simulating polymorphism data forward-in-time on the chromosome and genome level. Its most striking features are high runtime efficiency, specifically when a part of the sequence to be simulated shall be neutral. Furthermore, for the neutral part of the sequence, AnA-FiTS stores (and outputs) a graph structure that allows to reconstruct the ancestral part of each haplotype that survived into present at any point in time.
For installing AnA-FiTS, simply download the source tarball.
The most up-to-date version can be acquired from my github repository, however no guarantees about stability of the software can be made.
If requirements are fulfilled (see next section), installing AnA-FiTS should be as easy as
tar xfz ana-fits-1.0.3.tar.gz cd ana-fits-1.0.3 ./configure make
Currently, AnA-FiTS requires a 64-bit Linux system and a recent C++ compiler (gcc > 4.6 should do). Furthermore, you must have installed the boost library.
For instance on Debian/Ubuntu, this should be as easy as typing
sudo aptitude install libboost-all-dev
If boost is missing or too old, the ./configure will fail.
For a simple run with (relatively arbitrarily chosen) default parameters, simply enter
./Anafits -n runid -s <someSeedNumber>
into the terminal. AnA-FiTS will conduct the simulation and create a file containing the polymorphism data in ms-like output format, a graph file and an info file. The graph and polymorphism file are in binary and can be converted with
For an overview over the basic options, just call with the help flag
A walk-through and more detailed documentation (including some discussion about tuning parameters) can be found under in the manual that is included in the AnA-FiTS distribution (tarball).
Alternatively, check out the latest version of this manual in the github repository (see the doc folder).
For feature requests or bug reports, please send an email to andre dot aberer at h-its dot org (and of course replace everything in italique with the respective characters).