ASTRAL-Pro 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_pro_access astralpro_invoke1 perl $num_gtrees < 10000 && $num_taxa < 300 perl "astral-pro_1.16_expanse -t 16" 0 astralpro_invoke2 perl $num_gtrees < 10000 && $num_taxa > 299 && $num_taxa < 2000 perl "astral-pro_1.16_expanse -t 48 " 0 astralpro_invoke3 perl $num_gtrees < 10000 && $num_taxa > 1999 perl "astral-pro_1.16_expanse -t 4" 0 astralpro_invoke4 perl $num_gtrees > 9999 perl "astral-pro_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 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_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 mapping_file Select a mapping file (-a) mapping_file.txt perl (defined $value) ? "-a multitree_genename.map":"" 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. resolved_speciestree Place taxa on this fully resolved species tree (-c) perl (defined $resolved_speciestree) ? "-c resolved_speciestree.tre":"" resolved_speciestree.tre 18 resolved_speciestree2 Score and annotate the fully resolved species tree (-C) perl ( $value) ? "-C ":"" 8 This option scores the full species tree file after `-c` without exploring other topologies (`-r 1 -s 0`) 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) select_constraintfile Select a constraint file 30 constraint.tre perl (defined $value) ? "-c constraint.tre":"" Newick file containing a binary species tree to place missing species on select_guidetreefile Select a guidetree file 30 guidetree.tre perl (defined $value) ? "-g guidetree.tre":"" Newick file containing binary trees as guide trees results *