• C J R Illingworth.
• Department of Genetics, University of Cambridge, Cambridge CB2 3AS, UK.
• Bioinformatics. 2016 Jul 15; 32 (14): 2208-9.

UnlabelledAn increasingly common method for studying evolution is the collection of time-resolved short-read sequence data. Such datasets allow for the direct observation of rapid evolutionary processes, as might occur in natural microbial populations and in evolutionary experiments. In many circumstances, evolutionary pressure acting upon single variants can cause genomic changes at multiple nearby loci. SAMFIRE is an open-access software package for processing and analyzing sequence reads from time-resolved data, calling important single- and multi-locus variants over time, identifying alleles potentially affected by selection, calculating linkage disequilibrium statistics, performing haplotype reconstruction and exploiting time-resolved information to estimate the extent of uncertainty in reported genomic data.Availability And ImplementationC ++ code may be found at https://github.com/cjri/samfire/Contactchris.illingworth@gen.cam.ac.ukSupplementary InformationSupplementary data are available at Bioinformatics online.© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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