INRA, UMR85, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W479-85. doi: 10.1093/nar/gkr243. Epub 2011 Apr 29.
Evolutionary analyses of biological data are becoming a prerequisite in many fields of biology. At a time of high-throughput data analysis, phylogenetics is often a necessary complementary tool for biologists to understand, compare and identify the functions of sequences. But available bioinformatics tools are frequently not easy for non-specialists to use. We developed PhyleasProg (http://phyleasprog.inra.fr), a user-friendly web server as a turnkey tool dedicated to evolutionary analyses. PhyleasProg can help biologists with little experience in evolutionary methodologies by analysing their data in a simple and robust way, using methods corresponding to robust standards. Via a very intuitive web interface, users only need to enter a list of Ensembl protein IDs and a list of species as inputs. After dynamic computations, users have access to phylogenetic trees, positive/purifying selection data (on site and branch-site models), with a display of these results on the protein sequence and on a 3D structure model, and the synteny environment of related genes. This connection between different domains of phylogenetics opens the way to new biological analyses for the discovery of the function and structure of proteins.
生物数据的进化分析正在成为许多生物学领域的先决条件。在高通量数据分析的时代，系统发生学通常是生物学家理解、比较和识别序列功能的必要补充工具。但是，现有的生物信息学工具对于非专业人员来说往往不容易使用。我们开发了 PhyleasProg（http://phyleasprog.inra.fr），这是一个用户友好的网络服务器，是一种用于进化分析的即用型工具。PhyleasProg 可以通过以简单而稳健的方式分析数据，使用符合稳健标准的方法，帮助在进化方法方面经验有限的生物学家。通过非常直观的网络界面，用户只需输入一组 Ensembl 蛋白 ID 和一组物种作为输入。动态计算后，用户可以访问系统发育树、阳性/净化选择数据（在站点和分支站点模型上），并在蛋白质序列和 3D 结构模型上显示这些结果，以及相关基因的同线性环境。这种系统发生学不同领域之间的联系为发现蛋白质的功能和结构开辟了新的生物学分析途径。
