Software & Data | Department of Biology

Statistical & Computational Biology

Software

We strive to make all our developments available as user-friendly and open-source software. All software is available through git respositories, and all of them come with a detailed manual.

ABCtoolbox

ABCtoolbox is a general purpose tool to perform Approximate Bayesian Computation (ABC) estimations using a large set of algorithms. It is perfectly suited to conduct posterior inference and model choice using the robust ABC-GLM method we introduced and comes with an array of functionalities to properly validate an ABC application. Due to its potential to interact with almost any command line simulation software, ABCtoolbox can be used to study almost any problem for which a similation program is available.

Published version

ABCtoolbox can be obtained as a zipped file (ABCtoolbox.zip) here containg the source code, binaries for Linux and Windows and example files. A detailed description of ABCtoolbox is given in the manual, which is available here (ABCtoolbox_manual.pdf).

ABCtoolbox 2.0 (Beta)

We are currently working on a new version with vastly expanded functionalities, many bug corrections and general speed ups. This new version is provided through a git repository found at https://bitbucket.org/wegmannlab/abctoolbox-public/.

Citation: Wegmann D, Leuenberger C , Neuenschwander S & Excoffier L (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 11: 116.
ApproxWF

ApproxWF (Approximate Wright-Fisher) is a software that implements the mean transition time approximation of the Wright-Fisher model and allows to infer the effective population size along with locus specific selection coefficients from time series data. It is available through a git repository.

Citation:Ferrer-Admetlla A, Leuenberger C, Jensen JD, Wegmann D (2016). An Approximate Markov Model for the Wright-Fisher Diffusion and its Application to Time Series Data. Genetics 203(2): 831-846.
ATLAS

ATLAS, the Analysis Tools for Low coverage and Ancient Samples, is a software for the analysis of low coverage and ancient DNA sequences. This toolbox includes algorithms for quality score recalibration, variant calling and the inference of population genetic parameters such as local heterozygosity. ATLAS is available through a git repository.
Levolution

Levolution implements a computationally efficient method to infer the rate, strength and location of evolutionary jumps of quantitative traits on phylogenetic trees using Lévy processes. Levolution is available through a git repository.

Citation: Duchen P, Leuenberger C, Szilagyi SM, Harmon L, Eastman J, Schweizer M & Wegmann D (2017). Inference of evolutionary jumps in large phylogenies using Lévy processes. Systematic Biology, 66(6): 950–963.
poolStat

poolStat is a program to estimate population genetic statistics from pool-seq data. It si available through a git repository.
RASPberry

RASPberry is a software to infer recombination maps from admixed individuals, along with the ancestries along a chromosome. It is available through a git repository.

Citation: Wegmann D, Kessner D, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, Becker LC, Ruczinski I, Beaty TH, Kardia SLR, Meyers DA, Barnes KC, Becker DM, Freimer N and Novembre J (2011). Recombination rates in admixed individuals identified by ancestry-based inference. Nature Genetics 43(9): 847-853.
Tiger

The Tools to Integrate Genotyping Errors (Tiger) are a suite of routines that allow for the estimation of genoytping error rates from replicates or using a truth set, and to then update genotype likelihoods to reflect those errors. Tiger is available through our git repository.
Flink

Flink implements a selection scan based on the F-model and accounts for limkage between sites. Flink is available through our git repository.