Software

Tandem

Tandem is a utility tool that is useful in microsatellite analysis as it helps to bin microsatellite allele sizes in an internally consistent manner. A first version of Tandem is available as a Ruby script to be executed on the command line or as a minimal GUI program. Both of these are available from the website of the Salzburger Lab at the University of Basel and have been presented in Matschiner & Salzburger (2009).

A second version of Tandem, Tandem2, was developed for Mac OS with a more extensive graphical user interface that included the automated highlighting of problematic alleles and the possibility to edit these directly in the interface, as well as additional export options. However, Tandem2 was written in MacRuby, which unfortunately has not been supported by Mac OS newer than Mac OS Sierra. Thus, this new version may only be useful for users who still happen to run an old Mac OS.

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CladeAge

CladeAge is an add-on package for the Bayesian software BEAST 2 which allows time calibration of phylogenetic trees based on probability densities for clade ages, calculated from a model of constant diversification and fossil sampling. CladeAge has been presented and applied in Matschiner et al. (2017).

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F4

F4 is a Python script that can be useful for the identification of introgression signals from genomics data, as it calculates the f4-statistic from allele frequencies of four populations and uses coalescent simulations to test whether this value could be explained by incomplete lineage sorting alone. It has been developed for the study of Meyer et al. (2017) and is described in more detail on the associated GitHub repository.

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Fitchi

Fitchi is a Python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics. It has been presented in Matschiner (2016) and first applied in Runemark et al. (2018).

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Dsuite

Dsuite is a command-line tool that allows the quick calculation of D-statistics and related statistics from large genomic datasets, and is thus useful for the analysis of introgression. The tool has been developed by Milan Malinsky and Hannes Svardal with a minor contribution from Michael. Dsuite is described in more detail on the associated GitHub repository

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msprime

msprime is a tool written in C with a Python API, allowing coalescent simulations of genetic data under flexible population histories. It is developed and maintained by a large and international team of developers, led by Jerome Kelleher. A minor contribution from Michael consisted of code for species tree parsing. The msprime 1.0 version is described in a recent preprint by Baumdicker et al. (2021).

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