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This is the homepage of clonalframeml, a software package that performs efficient inference of recombination in bacterial genomes The software can be applied to any type of aligned nucleotide sequence data, but is especially aimed at analysis of whole genome sequences. Clonalframeml was created by xavier didelot and daniel wilson.

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ClonalFrameML: 整合细菌全基因组重组推理工具项目介绍ClonalFrameML是由Xavier Didelot和Daniel Wilson开发的一款高效细菌全基因组重组推断软件包。它设计用于分析细菌微进化，特别是通过多位点序列数据来识别样本间的克隆关系，并估算同源重组事件在染色体上的位置。 Clonalframeml was created by xavier didelot and daniel wilson Here we present clonalframeml, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction.

以上就是对ClonalFrameML项目的基本结构、启动方法以及配置方式的简单介绍。更深入的使用细节，包括具体的参数使用和数据分析流程，应当参考正式的用户指南和项目文档。

In 2015 a new separate software was released called clonalframeml which is designed to run on large whole genomes datasets For more information about clonalframeml, see the separate clonalframeml website. This document provides a technical overview of clonalframeml, a software package for efficient maximum likelihood inference of recombination in bacterial genomes.