1.10 A lightweight python library to predict the difficulty of Multiple Sequence Alignments Julia Haag Haag, J., Höhler, D., Bettisworth, B., and Stamatakis, A. (2022). From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses. Molecular Biology and Evolution, 39(12). Phylogeny pythia_access invoke_run perl "pythia_1.0.0_expanse" 0 infile perl "-m MSA.txt -b -v" MSA.txt scheduler_input scheduler.conf perl !$more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=16G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" scheduler_input2 scheduler.conf perl $more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=128G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" all_outputfiles * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 perl "runhours=$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 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. more_memory 1 I need more memory This job will require 64 cpus as configured, if it runs for the full time, it will consume $runtime x 64 cpu hours. perl $more_memory This job will require 8 cpus as configured, if it runs for the full time, it will consume $runtime x 8 cpu hours. perl !$more_memory specify_Precision 2 Set the number of decimals the difficulty should be rounded to (-prec) perl (defined $value) ? "-prec $value":"" 2 Set the number of decimals the difficulty should be rounded to. Recommended and default is 2. specify_storeTrees 2 Store Parsimony Trees (-sT) perl ($value) ? "-sT":"" If set, stores the parsimony trees as '{msa_name}.parsimony.trees' file. specify_removeDups Remove duplicate sequences, (--removeDuplicates) perl ($value) ? "--removeDuplicates ":"" 1 Pythia refuses to predict the difficulty for MSAs containing duplicate sequences. If this option is set, PyPythia removes the duplicate sequences, stores the reduced MSA as '{msa_name}.{phy/fasta}.pythia.reduced' and predicts the difficulty for the reduced alignment.