3.6.4 Analyzing and reconstructing reticulate evolutionary relationships - run on XSEDE Than, C., Ruths, D., and Nakhleh, L. Zhu, J., and Nakhleh, L. (2018) Inference of Species Phylogenies from Bi-allelic Markers Using Pseudo-likelihood. bioRxiv Zhu, J., Wen, D., Yu, Y., Meudt, H. M., and Nakhleh, L. (2018) Bayesian inference of phylogenetic networks from bi-allelic genetic markers. PLOS Computational Biology 14, e1005932 Wen, D., Yu, Y., and Nakhleh, L. (2016) Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. PLOS Genetics 12, e1006006 Yu, Y., and Nakhleh, L. (2015) A maximum pseudo-likelihood approach for phylogenetic networks. BMC Genomics 16, S10. Yu, Y., and Nakhleh, L. (2015) A maximum pseudo-likelihood approach for phylogenetic networks. BMC Genomics 16, S10. Yu, Y., Barnett, R. M., and Nakhleh, L. (2013) Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. Systematic Biology 62, 738-751 Than, C., Ruths, D., and Nakhleh, L. (2008) PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9, 322-322 Phylogeny / Alignment phylonet_xsede invocation1 perl "phylonet_3.6.4" 0 infile Input Data (Nexus File) perl "script.nex" script.nex ALL_FILES * gpu_option 1 scheduler.conf perl $use_gpu perl "gpu=1\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" . "runhours=$runtime\\n" no_gpu_option 1 scheduler.conf perl !$use_gpu perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=$num_processors\\n" . "runhours=$runtime\\n" runtime 1 Maximum Hours to Run (click here for help setting this correctly) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 Please enter a positive number for the maximum runtime perl $runtime < 0 Please specify a maximum runtime perl !defined $runtime Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. num_processors How many processors did you specify? 1 use_gpu Use a GPU 0