Author: Yixuan Guo, Haoyang Wu, Yang Liu, Rebecca J. Stones, Gang Wang, Xiaoguang Liu, Qiang Xie. Nankai University, 94 Weijin Road, Tianjin 300071, China. We present PhyloPipe, a graphical pipe-lining software for phylogenomic analysis. PhyloPipe combines a collection of widely used software in phylogenomic research, HaMStR, MAFFT, MUSCLE, Aliscore and RaxmlGUI, together with intermediate procedures into an integrated pipeline. It provides a graphical user interface manipulating the compiled input files of annotated transcriptomic data into a RAxML-compatible format, which can be used to generate a phylogenetic tree. Directory Structure: 1. PhyloPipe_QTProject This is the source codes of PhyloPipe project. The software is built on QTCreator development platform on CentOS6.5 Operating System. 2. PhyloPipe.v1.1 This is the current stable version of PhyloPipe, can be directly activated via double-click on Linux environment. 3. PhyloPipe.v1.1_manual_20150610.pdf This is the manual for PhyloPipe v1.1, preparation and useage case is illustrated in this manual file. 4. PhyloPipe.v1.1_manuscript_20150610.pdf This is the manuscript of PhyloPipe v1.1 in BMC Bioinformatics format. PhyloPipe flowchart and key algorithms is elaborated in this manuascript. If you have any suggestions about PhyloPipe, please contact me at guoyixuan@nbjl.nankai.edu.cn.