COMPASS: the COMPletely Arbitrary Sequence Simulator

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2017 Jun 6

PMID 28582485

Citations 1

Authors

Andrew Low

Nicolas Rodrigue

Alex Wong

Affiliations

Soon will be listed here.

Abstract

Summary: 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 http://labs.carleton.ca/eme/software-and-data.

Contact: alex_wong@carleton.ca.

Supplementary Information: Supplementary data are available at Bioinformatics online.

Citing Articles

The search of sequence variants using a constrained protein evolution simulation approach.

Tuffery P, de Vries S Comput Struct Biotechnol J. 2020; 18:1790-1799.

PMID: 32695271 PMC: 7355721. DOI: 10.1016/j.csbj.2020.06.018.

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