1.0 Extract optimal recombination-filtered blocks (no four-gamete violations) from recombination-rich genomic re-sequence data Woerner, A. E., Cox, M. P., and Hammer, M. F. Woerner, A. E., Cox, M. P., and Hammer, M. F. (2007) Recombination-filtered genomic datasets by information maximization. Bioinformatics 23, 1851-1853. 10.1093/bioinformatics/btm253 Phylogeny / Alignment imgc_xsede imgc_expanse perl "/expanse/projects/ngbt/opt/expanse/IMgc/IMgc.pl" 0 number_nodes_patlt10000 2 scheduler.conf perl "ChargeFactor=1.0\\n" . "no_stdout_saved=1\\n" . "mem=5G\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" infile Input File (must be in fasta format) perl "infile.fas" 5 infile.fas all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours for non-gpu; 120 for gpu jobs) perl "runhours=$value\\n" 0.5 The maximum runtime can be no more than 168 hours perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 The job will run on 1 processors as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl $runtime > 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 dependably 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. maintain_seqlength Weed out individuals; maintains original sequence length (fast; -w) perl $value ? "-w":"" 0 10 weed_individandsites Weed out both individuals and sites; make the largest block possible; (slow, -s)] perl $value ? "-s":"" 1 11 weight_keepindivid Weight keeping individuals -i perl (defined $value) ? "-i $value":"" 1 12 omit_nthid Omit the nth id from the fasta file when optimizing perl (defined $value) ? "-o $value":"" 13 Omits the nth id from your fasta file when optimizing the region, but tacks them back on in the output preserve_pthid Preserve the pth id perl (defined $value) ? "-p $value":"" 14 Preserves the pth id from your fasta file no matter what print_fatsaformat Print the output in fasta format (-f) perl ($value) ? "-f":"" 1 16