1.01 Address MSA uncertainty and error with software run on XSEDE R.H. Ali, M. Bogus, S. Whelan Ali RH, Bogusz M, Whelan S. Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. Mol Biol Evol. 2019 Oct 1;36(10):2340-2351. doi: 10.1093/molbev/msz142. PMID: 31209473; PMCID: PMC6933875. Phylogeny / divvier_xsede invoke_run perl "/expanse/projects/ngbt/opt/expanse/divvier/Divvier/divvier" 0 infile Sequences File (relaxed phylip format) (-in) perl "infile.txt" 99 infile.txt scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=7G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" all_outputfiles * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 perl "runhours=$value\\n" Maximum Hours to Run must be less than 168 perl $runtime > 168 Maximum Hours to Run must be greater than 0 perl $runtime < 0 Please Enter a Value for Maximum Hours to Run perl !defined $runtime 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 $runtime > 0 Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. divv_orpartial 2 Select the algorithm divvy Divvy partial Partial perl "-$value" divvy Please select an algorithm: divvy or partial perl !defined $divv_orpartial This selects the algorithm, -divvy do standard divvying (DEFAULT); -partial: do partial filtering by testing removal of individual characters divvy_threshold Set the divvy threshold (--thresh) perl $divv_orpartial eq "divvy" perl $divvy_threshold ne $vdef ? "-thresh $value" : "" 0.801 6 partial_threshold Set the partial threshold (--thresh) perl $divv_orpartial eq "partial" perl $partial_threshold ne $vdef ? "--thresh $value" : "" 0.774 6 specify_minchars Minimum number of characters tested in a split (-approx) perl "-approx $value" 10 7 specify_checksplit Ensure there is a pair for every split (-checksplits) perl $value ? "-checksplits":"" 0 Go through sequence and ensure there's a pair for every split. This can be slow 8 specify_HMMexact Do the full pairHMM and ignore bounding (-HMMexact) perl $value ? "-HMMexact":"" 0 Check this to get -HMMexact: Do the full pairHMM and ignore bounding; uncheck to get the default, -HMMapprox: Do the pairHMM bounding approximation (DEFAULT) 9 specify_mincolumns Minimum number of characters in a column to output when divvying/filtering (-mincol) perl (defined $specify_mincolumns) ? "-mincol $specify_mincolumns":"" 2 10 output_gap Output a gap instead of the static * character (-divvygap) perl ($output_gap) ? "-divvygap":"" 1 11