3.1 Fast (Approximate) Maximum Likelihood tree construction - run on XSEDE H. Ashkenazy, O. Penn, O. et al. Ashkenazy, H., Penn, O., Doron-Faigenboim, A., Cohen, O., Cannarozzi, G., Zomer, O., and Pupko, T. (2012) FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res 40, W580-W584 Phylogeny / Alignment fastml_xsede fastml_comet perl "" 0 number_nodes 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\n" . "threads_per_process=1\\n" infile Input File (Fasta or interleaved PHYLIP format.) infile 99 infile all_results * runtime 1 Maximum Hours to Run (up to 168 hours) scheduler.conf 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 x $runtime cpu hours perl $runtime ne 0 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. datatype 5 Please Specify your data type nuc Nucleotide aa Amino acid codon codon nuc perl "--seqType $value " This option will help the application determine how to run the job intree Starting Tree in Newick Format (-intree) 5 perl (defined $value) ? "--Tree starting_tree": "" starting_tree -intree newick_file to set the starting tree. Tree must be in Newick format tree_algorithm perl !defined $intree perl "--TreeAlg NJ" dna_matrix Choose a DNA matrix(--SubMatrix) perl $datatype eq "nuc" JC_Nuc JC_Nuc T92 T92 HKY HKY GTR GTR JC_Nuc perl "--SubMatrix $value" protein_matrix Choose a Protein matrix(--SubMatrix) perl $datatype eq "aa" JTT JTT LG LG mtREV mtREV cpREV cpREV WAG WAG DAYHOFF DAYHOFF JTT perl "--SubMatrix $value" codon_matrix Choose a Protein matrix(--SubMatrix) perl $datatype eq "codon" yang Yang empiriCodon EmpiriCodon yang perl "--SubMatrix $value" optimize_branchlengths Optimize Branch Lengths (--OptimizeBL) 5 perl ($value) ? "--OptimizeBL":"" 1 use_gamma Use Gamma (--UseGamma) 5 perl ($value) ? "--UseGamma":"" 1 specify_alpha Specify Alpha (--Alpha) perl $use_gamma perl (defined $value) ? "--Alpha $value":"" User specifies the alpha parameter of the gamma distribution [if alpha is not given, alpha and branches will be evaluated from the data] joint_reconstruction Joint_reconstruction (--jointReconstruction) perl ($value) ? "--jointReconstruction":"" User specifies the alpha parameter of the gamma distribution [if alpha is not given, alpha and branches will be evaluated from the data] indel_reconstruction Method for Indel_reconstruction (--indelReconstruction) PARSIMONY Parsimony ML ML BOTH Both perl (defined $value) ? "--indelReconstruction $value":"" indel_cutoff Cutoff for Indel vs Char (--indelCutoff) perl ($value) ? "--indelCutoff":""