1 A new strategy for rapidly aligning millions of sequences Tong Zhou, Pinglu Zhang, Quan Zou, Wu Han HAlign 4: a new strategy for rapidly aligning millions of sequences, Tong Zhou, Pinglu Zhang, Quan Zou, Wu Han, Bioinformatics, Volume 40, Issue 12, December 2024, btae718, https://doi.org/10.1093/ Phylogeny/Sequence Alignment halign4_access halign4_1 perl "halign4_expanse " 1 mpi_processes_conf1 3 scheduler.conf perl !$scriptfile_specifies perl "jobtype=mpi\\n" . "cpus-per-task=16\\n" . "mem=32G\\n" . "node_exclusive=0\\n" . "mpi_processes=1\\n" infile Input File (must be in Nexus format) (-execute) infile.fasta perl "infile.fasta output.fasta -t 16" 5 ALL_FILES * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 168 The maximum hours to run must be less than 168 perl $runtime > 168.0 Please enter a positive number for the maximum runtime perl $runtime < 0 Please specify a maximum runtime perl !defined $runtime perl "runhours=$value\\n" The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl $runtime > 0 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. specify_reference Specify the reference sequence name (-r, no whitespace allowed) perl "-r $value" 10 The longest sequence will used as reference. White spaces are not allowed in sequence names perl !defined $specify_reference specify_globalsa Specify the Global SA threshold (-sa default=15) perl (defined $specify_globalsa) ? "-sa $value":"" 15 15