Illingworth C J R
Department of Genetics, University of Cambridge, Cambridge CB2 3AS, UK.
Bioinformatics. 2016 Jul 15;32(14):2208-9. doi: 10.1093/bioinformatics/btw205. Epub 2016 Apr 22.
An 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.
C ++ code may be found at https://github.com/cjri/samfire/
chris.illingworth@gen.cam.ac.uk
Supplementary data are available at Bioinformatics online.
一种日益常见的研究进化的方法是收集时间分辨短读长序列数据。此类数据集能够直接观察快速进化过程，比如自然微生物群体和进化实验中可能出现的情况。在许多情况下，作用于单个变异体的进化压力会导致多个相邻位点的基因组变化。SAMFIRE是一个开放获取的软件包，用于处理和分析来自时间分辨数据的序列读数，随时间推移识别重要的单基因座和多基因座变异体，鉴定可能受选择影响的等位基因，计算连锁不平衡统计量，进行单倍型重建，并利用时间分辨信息来估计所报告基因组数据中的不确定性程度。
C++代码可在https://github.com/cjri/samfire/获取。
chris.illingworth@gen.cam.ac.uk
补充数据可在《生物信息学》在线获取。
