COMPASS: the COMPletely Arbitrary Sequence Simulator

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Simulated sequence alignments are frequently used to test bioinformatics tools, but current sequence simulators are limited to defined state spaces. Here, we present the COMPletely Arbitrary Sequence Simulator (COMPASS), which is able to simulate the evolution of absolutely any discrete state space along a tree, for any form of time-reversible model.

Availability and implementation:

COMPASS is implemented in Python 2.7, and is freely available for all platforms with the Supplementary Information, as well as at


Supplementary information:

Supplementary data are available at Bioinformatics online.

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