Integrated Pipeline for Phylogenetic Analysis of Vertebrate Gene Families

Abstract

Gene phylogenetic analysis is a valuable study that can find out the difference in existence behaviours of genes in different species, reveal the evolutionary relationships among gene family members and reflect the divergence level and time between groups of gene family members or genes. Yet the procedures involved are extremely time consuming and labour-intensive. In this project, I analysed the existing methods of each process and designed a workflow of the phylogenetic analysis process by implementing a set of analysis modules and connect them in series. I proposed an integrated gene phylogenetic analysis pipeline (PGAP) which can carry out the entire phylogenetic analysis for the genes of interest automatically. It is also equipped with an interactive visualization interface that can instantly project the analysis result provided after the analysis layers finishes the computation, and allows user to manipulate the details of visualization scenarios within certain scope. The pipeline has an attached web-application based interface, where users can upload their query protein sequences, setting parameters for different analysis modules included in PGAP. The implementation of analysis modules in PGAP takes advantages of widely recognized algorithms for each task, which are concatenated together to be an effective, efficient and productive tool. A dynamic-programming-based phylogenetic tree restructure algorithm is also proposed during the development, with time complexity of O(n4). PGAP reduce the workload of phylogenetic analysis from many researchers' working months to days of data-intensive computations. It is more than a production tool for phylogenetic analysis researchers, but a great helper to the beginners' study in bioinformatics area. It aims to emancipate more production, and managed to address the real problem that may tackle the continuous development of gene phylogenetic study.