MOTIVATION: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. RESULTS: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a user-friendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. AVAILABILITY AND IMPLEMENTATION: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems.
MOTIVATION: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. RESULTS: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a user-friendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. AVAILABILITY AND IMPLEMENTATION: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems.
Authors: Wei Shi; Lingshu Wang; Tongqing Zhou; Mallika Sastry; Eun Sung Yang; Yi Zhang; Man Chen; Xuejun Chen; Misook Choe; Adrian Creanga; Kwan Leung; Adam S Olia; Amarendra Pegu; Reda Rawi; Chen-Hsiang Shen; Erik-Stephane D Stancofski; Chloe Adrienna Talana; I-Ting Teng; Shuishu Wang; Kizzmekia S Corbett; Yaroslav Tsybovsky; John R Mascola; Peter D Kwong Journal: bioRxiv Date: 2022-01-26