Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes
Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes
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Coinfinder：检测泛基因组中的显着关联和解离
DOI：
10.1101/859371
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Whelan F
中科院分区：
文献类型：
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作者：
Whelan F
原核生物和真核生物泛基因组的辅助基因通过水平基因转移、差异基因丢失以及选择和漂变效应积累。我们已经开发了Coinfinder，这是一种软件程序，可以评估泛基因组中的同源基因（基因家族）是否比偶然预期的更频繁地相互关联或解离（即“巧合”）。Coinfinder使用用户提供的系统发育树来评估每个辅助基因的谱系依赖性（即系统发育分布），使Coinfinder能够专注于重合的基因对，这些基因对的联合存在不仅仅是因为它们碰巧出现在同一个进化枝中，而是因为它们往往比预期的更经常出现在同一个进化枝中。Coinfinder是用C++、Python3和R实现的，可以在https://github.com/fwhelan/coinfinder的GNU许可证下免费获得。
The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are ‘coincident’) more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.