We present Phylogenetic Graph (PhyG), an open-source, phylogenetic search tool for diverse data types and graphs, including softwired and hardwired networks, in addition to trees. This allows for analysis of horizontal transfer and hybridization scenarios, as well as the necessary vertical inheritance of trees. PhyG is the successor to POY5 in performing combined data tree-alignment with enhancements in heuristic optimality (up to 7% in example data) and execution time (up to a factor of 200). Input data may exhibit a practically unlimited number of character states in qualitative or sequence (aligned and unaligned) types. Novel graph construction and refinement algorithms have been implemented and integrated into a variety of search procedures. Currently, PhyG implements parsimony and No-Common-Mechanism Likelihood optimization.

中文翻译：

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PhylogenesisGraph (PhyG) 一个新的系统发育图搜索和优化程序

我们推出了系统发育图（PhyG），这是一种开源的系统发育搜索工具，适用于多种数据类型和图表，除了树之外，还包括软连线和硬连线网络。这允许分析水平转移和杂交场景，以及树的必要垂直继承。PhyG在执行组合数据树对齐方面是POY5的后继者，并增强了启发式最优性（示例数据中高达 7%）和执行时间（高达 200 倍）。输入数据可以表现出实际上无限数量的定性或序列（对齐和未对齐）类型的字符状态。新颖的图构建和细化算法已被实现并集成到各种搜索程序中。目前，PhyG实现了简约性和非通用机制似然优化。