ASTRAL-Hybrid on ACCESS 1.16 Species tree reconstruction Chao Zhang and Siavash Mirab Chao Zhang and Siavash Mirarab (2022) ASTRAL-Pro 2: Ultrafast species tree reconstruction from multi-copy gene family trees. Bioinformatics 38(21) 4949–4950, https://doi.org/10.1093/bioinformatics/btac620 Phylogeny / Alignment astral_hybrid_access astralhyb_invoke1 perl $num_gtrees < 10000 && $num_taxa < 300 perl "astral-hybrid_1.16_expanse -t 16" 0 astralhyb_invoke2 perl $num_gtrees < 10000 && $num_taxa > 299 && $num_taxa < 2000 perl "astral-hybrid_1.16_expanse -t 48 " 0 astralhyb_invoke3 perl $num_gtrees < 10000 && $num_taxa > 1999 perl "astral-hybrid_1.16_expanse -t 4" 0 astralhyb_invoke4 perl $num_gtrees > 9999 perl "astral-hybrid_1.16_expanse -t 8" 0 number_cores1 2 scheduler.conf perl $num_gtrees < 10000 && $num_taxa < 300 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=32G\\n" . "node_exclusive=0\\n" . "cpus-per-task=16\\n" . "threads_per_process=16\\n" number_cores2 2 scheduler.conf perl $num_gtrees < 10000 && $num_taxa > 299 && $num_taxa < 2000 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=96G\\n" . "node_exclusive=0\\n" . "cpus-per-task=48\\n" . "threads_per_process=48\\n" number_cores3 2 scheduler.conf perl $num_gtrees < 10000 && $num_taxa > 1999 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=8G\\n" . "node_exclusive=0\\n" . "cpus-per-task=4\\n" . "threads_per_process=4\\n" number_cores2 2 scheduler.conf perl $num_gtrees > 9999 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=16G\\n" . "node_exclusive=0\\n" . "cpus-per-task=8\\n" . "threads_per_process=8\\n" infile Input genetrees.tre 1 infile_invoke Input perl "-i genetrees.tre" 99 write_log 99 perl " 2> multitree.nw.log" verbose_logging 16 perl " -v 2" runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 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 16 processors as configured. If it runs for the entire configured time, it will consume 16 x $runtime cpu hours perl $num_gtrees < 10000 && $num_taxa < 300 The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $num_gtrees < 10000 && $num_taxa > 299 && $num_taxa < 2000 The job will run on 4 processors as configured. If it runs for the entire configured time, it will consume 4 x $runtime cpu hours perl $num_gtrees < 10000 && $num_taxa > 1999 The job will run on 8 processors as configured. If it runs for the entire configured time, it will consume 8 x $runtime cpu hours perl $num_gtrees > 9999 Estimate the maximum time your job will need to run. We recommend testing 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_gtrees Number of Gene trees in your input file Please specify the number of gene trees in your sample perl !defined $num_gtrees num_taxa Number of taxa in your input file Please specify the number of unique taxa in your samples perl !defined $num_taxa specify_preset Use a preset mode -C -B -S -L -R perl (defined $value) ? "$value":"" 8 outfile_name Output file name perl (defined $value) ? "-o $value":"" multitree.nw.output Please specify a name for your outputfile perl !defined $outfile_name 8 Specify a filename for storing the output species tree. specify_searchrounds Set the number of search rounds (-r) perl (defined $value) ? "-r $value":"" 4 8 specify_subsamples Set the number of subsamplings (-s) perl (defined $value) ? "-s $value":"" 4 8 specify_minsupportval Min possible support value in weight scale (-n) perl (defined $value) ? "-n $value":"" 0 8 specify_maxsupportval Maximum possible support value in weight scale (-x) perl (defined $value) ? "-x $value":"" 100 8 specify_defaultfloat Default support value when weight not provided (-d) perl (defined $value) ? "-d $value":"" 0 8 specify_proportion Proportion of taxa in the subsample in naive algorithm (--proportion) perl (defined $value) ? "--proportion $value":"" 0.25 8 resolved_speciestree Place taxa on this fully resolved species tree (-c) perl (defined $resolved_speciestree) ? "-c resolved_speciestree.tre":"" resolved_speciestree.tre 18 specify_guidetree Use a guide tree (-g) perl (defined $resolved_speciestree) ? "-g guidetree.tre":"" guidetree.tre 18 mapping_file Select a mapping file (-a) mapping_file.txt perl (defined $value) ? "-a multitree_genename.map":"" The -a option requires a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab 8 specify_seed Specify a seed value (-seed) perl (defined $value) ? "--seed $value":"" 12 Seed for pseudorandomness specify_root Root at this species (-root) perl (defined $value) ? "--root $value":"" 12 Root at the given species specify_supportopt Output support option (-u) 0 1 2 3 perl (defined $value) ? "-u $value":"" 1 10 Select No output support if you want to compute species tree topology only; Select Detailed if you support and local-PP for all three resolutions of each branch.. specify_downweightrepeat Number of trees sampled for each locus. (-w) perl (defined $value) ? "-w $value":"" 1 12 specify_lambda Set the lambda parameter for the Yule prior. (-l) perl (defined $value) ? "-l $value":"" 0.5 12 Set the lambda parameter for the Yule prior used in the calculations of branch lengths and posterior probabilities. Set to zero to get ML branch lengths instead of MAP. Higher values tend to shorten estimated branch lengths and very high values can give inaccurate results (or even result in underflow). (default: 0.5) specify_treeweights Specify a list of gene tree weights (--treeweights) 30 perl (defined $value) ? "--treeweights treeweights.tre":"" treeweights.tre A list of gene tree weights, space/tab/new-line separated (default: uniform weights) specify_mode Specify your weithing mode (--mode) 30 1 2 3 4 perl (defined $value) ? "--mode $value":"" 1 results *