The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms. CAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein’s function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib . CAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.

中文翻译：

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CAPRIB：一种用户友好的工具，用于研究氨基酸变化和选择，以探索属内进化

细菌的进化受到不同机制的影响，例如突变、基因缺失、复制或外源 DNA 插入等。作为自然选择的结果，这些遗传变化可以在后代中积累。使用系统发育和基因组比较，可以以某种方式追溯进化路径，最近发生的事件比旧事件更容易检测到。出于这个原因，有多种工具可用于研究单个物种基因组内的进化事件，例如基因组成改变，或 SNP 等更微妙的突变。然而，这些工具通常旨在比较相似的基因组，并且需要生物信息学方面的高级技能。我们介绍了 CAPRIB，这是一种用 Java 开发的独特工具，可以在属水平上确定氨基酸的变化，这与两组生物之间的表型差异相关。CAPRIB 具有用户友好的图形界面并使用 SQL 数据库，无需编程或全面的生物信息学知识即可轻松比较多个基因组。这个直观的软件缩小了在属范围内与给定表型差异相伴的氨基酸变化列表。我们的软件发现的每个排列都与两个已描述的统计值相关联，这些统计值表明其对蛋白质功能的潜在影响，帮助用户决定进一步研究哪些有希望的候选者。我们证明 CAPRIB 能够检测已知突变并发现更多，并且该工具可用于质疑分子系统发育。最后，我们通过精确定位与快速生长的分枝杆菌出现缓慢生长的分枝杆菌同时发生的氨基酸变化来举例说明 CAPRIB 的效用。该软件可在 https://github.com/BactSymEvol/Caprib 免费获得。CAPRIB 是一种新的生物信息学软件，旨在使所有人都可以进行属规模比较。凭借其直观的图形界面，该工具可识别伴随表型差异的关键氨基酸变化。通过比较快速和缓慢生长的分枝杆菌，我们阐明了进化热点，例如细胞分裂素途径，它们是进一步实验的有趣候选者。CAPRIB 是一种新的生物信息学软件，旨在使所有人都可以进行属规模比较。凭借其直观的图形界面，该工具可识别伴随表型差异的关键氨基酸变化。通过比较快速和缓慢生长的分枝杆菌，我们阐明了进化热点，例如细胞分裂素途径，它们是进一步实验的有趣候选者。CAPRIB 是一种新的生物信息学软件，旨在使所有人都可以进行属规模比较。凭借其直观的图形界面，该工具可识别伴随表型差异的关键氨基酸变化。通过比较快速和缓慢生长的分枝杆菌，我们阐明了进化热点，例如细胞分裂素途径，它们是进一步实验的有趣候选者。