BACKGROUND Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. RESULTS Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. CONCLUSIONS Suitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees.

中文翻译：

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系统发育分析中的分裂诱导插入缺失。

背景大多数使用分子数据的系统发育研究将多个序列比对中的空位视为缺失数据，甚至完全排除包含空位的比对列。结果 在这里，我们展示了大规模、全基因组比对中的间隙模式本身具有系统发育信息，如果间隙数据经过适当过滤以减少比对方法引入的噪声，则可用于推断可靠的系统发育。我们在这里介绍分裂诱导插入缺失（splids）的概念，它定义了分类群集的近似二分法。我们在模拟数据和真实数据的案例研究中都表明，可以从系统基因组数据集中有效地提取 spids。