Department of Information Sciences, Tokyo University of Science, Noda City, Chiba, 278-8510, Japan.
BMC Bioinformatics. 2021 Jan 30;22(1):36. doi: 10.1186/s12859-021-03978-z.
Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates.
We introduced a new measure for estimating genetic differences, and presented PROP, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using PROP, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies.
PROP is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of PROP is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP .
系统发育分析强烈依赖于进化模型。大多数用于估计遗传差异和系统发育关系的进化模型都不处理序列比对中的空位。适当将包含插入和缺失的位点的进化信息纳入遗传差异度量中，将提高系统发育估计的准确性。
我们引入了一种新的遗传差异估计方法，并提出了 PROP，这是一个基于遗传差异的网站应用程序，可在考虑空位影响的情况下进行系统发育分析。作为使用 PROP 进行系统发育分析的示例，我们使用了 31 个生物体的完整 p53 氨基酸序列，并说明了包含空位的位点的信息是否纳入遗传差异会导致具有不同拓扑结构的树。
PROP 可在 https://www.rs.tus.ac.jp/bioinformatics/prop 上获得，用户可以通过在网站上上传序列数据来进行系统发育分析。PROP 的最显著特点是其遗传差异估计方法，无需消除对齐序列中的空位，这有助于用户在进化过程中检测到有意义的差异。源代码可在 GitHub 上获得：https://github.com/TUS-Satolab/PROP。
