PDF(Pubmed)
Abstract：
BACKGROUND: SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation.
RESULTS: Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool.
CONCLUSIONS: SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca , where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at https://github.com/UdeS-CoBIUS/SimSpliceEvol .
RESULTS: Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool.
CONCLUSIONS: SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca , where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at https://github.com/UdeS-CoBIUS/SimSpliceEvol .
摘要：
背景：SimSpliceEvol是一种用于模拟整合外显子-内含子结构进化的真核基因序列的进化以及从基因产生的转录物组的进化的工具。它以指导基因树作为输入，并为树的每个节点生成带有其转录本的基因序列，从根到叶子。然而,在引导基因树的不同节点模拟的转录本集缺乏进化联系。因此,SimSpliceEvol不适用于评估依赖于转录本保守性的转录系统发育推断或基因系统发育推断的方法。
结果：这里，我们介绍SimSpliceEvol2，与第一个版本相比，结合了一个明确的转录本进化模型，用于模拟引导基因树分支上的替代转录本，以及推断的转录系统发育。我们提供具有图形用户界面和Web服务器更新版本的全面软件，确保容易和用户友好的访问工具。
结论：SimSpliceEvol2生成合成数据集，可用于评估剪接RNA序列分析的方法和工具，如拼接对齐方法，鉴定保守转录本的方法，和转录系统发育重建方法。Web服务器可在https://simspliceevol访问。cobius.usherbrooke.ca,在那里你也可以下载独立的软件。该软件的全面文档可在同一地址获得。对于对源代码感兴趣的开发人员，这需要安装所有先决条件才能运行，它在https://github.com/UdeS-CoBIUS/SimSpliceEvol提供。
结果：这里，我们介绍SimSpliceEvol2，与第一个版本相比，结合了一个明确的转录本进化模型，用于模拟引导基因树分支上的替代转录本，以及推断的转录系统发育。我们提供具有图形用户界面和Web服务器更新版本的全面软件，确保容易和用户友好的访问工具。
结论：SimSpliceEvol2生成合成数据集，可用于评估剪接RNA序列分析的方法和工具，如拼接对齐方法，鉴定保守转录本的方法，和转录系统发育重建方法。Web服务器可在https://simspliceevol访问。cobius.usherbrooke.ca,在那里你也可以下载独立的软件。该软件的全面文档可在同一地址获得。对于对源代码感兴趣的开发人员，这需要安装所有先决条件才能运行，它在https://github.com/UdeS-CoBIUS/SimSpliceEvol提供。
