The Exelixis Lab

Enabling Research in Evolutionary Biology

AnA-FiTS: Efficient Forward-in-Time Simulation of Polymorphism Data

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.

1 Installation

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

2 Requirements

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.

3 Quick Start

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

./convertSeq <file>


./convertGraph <file>


4 Documentation

For an overview over the basic options, just call with the help flag

./Anafits --help

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).

5 Contact

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).