RAxML-NG 1.0.1 RAxML-NG offers improvements in speed, flexibility and user-friendliness over previous RAxML versions. Alexey M. Kozlov, Diego Darriba, Tomas Flouri, Benoit Morel, and Alexandros Stamatakis Alexey M. Kozlov, Diego Darriba, Tomas Flouri, Benoit Morel, and Alexandros Stamatakis (2019) RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, btz305 doi:10.1093/bioinformatics/btz305 Phylogeny / Alignment https://github.com/amkozlov/raxml-ng raxmlng_xsede raxmlng_1 perl $select_analysis ne "J" && $select_analysis ne "I" && $select_analysis ne "fb" && $select_analysis ne "rfdist" perl "raxml-ng_1.1.0_expanse -msa infile.txt" 0 raxmlng_2 perl $select_analysis eq "J" || $select_analysis eq "I" || $select_analysis eq "fb" || $select_analysis eq "rfdist" perl "raxml-ng_1.1.0_expanse" 0 raxmlng__scheduler_mainnp1 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns < 4000 perl "threads_per_process=80\\n" . "mem=154G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainnp1worker perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns < 4000 perl "--workers 20" 1 raxmlng__scheduler_mainnp2 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $num_patterns < 8000 perl "threads_per_process=120\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainnp2workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $num_patterns < 8000 perl "--workers 20" 1 raxmlng__scheduler_mainnp3 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 7999 && $num_patterns < 40000 perl "threads_per_process=120\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainnp3workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 7999 && $num_patterns < 40000 perl "--workers 10" 1 raxmlng__scheduler_mainnp4 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 39999 && $num_patterns < 100000 perl "threads_per_process=125\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainnp4workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 39999 && $num_patterns < 100000 perl "--workers 5" 1 raxmlng__scheduler_mainnp5 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 99999 && $num_patterns < 500000 perl "threads_per_process=128\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainnp5workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns < 500000 && $num_patterns > 99999 perl "--workers 2" 1 raxmlng__scheduler_mainnp6 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 499999 perl "threads_per_process=128\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainnp6workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 499999 perl "--workers 1" 1 raxmlng__scheduler_mainpr1 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns < 1500 perl "threads_per_process=80\\n" . "mem=154G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainpr1workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns < 1500 perl "--workers 20" 1 raxmlng__scheduler_mainpr2 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $num_patterns < 5000 perl "threads_per_process=120\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainpr2workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $num_patterns < 5000 perl "--workers 20" 1 raxmlng__scheduler_mainpr3 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 4999 && $num_patterns < 10000 perl "threads_per_process=120\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainpr3workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 4999 && $num_patterns < 10000 perl "--workers 10" 1 raxmlng__scheduler_mainpr4 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 9999 && $num_patterns < 40000 perl "threads_per_process=125\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainpr4workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 9999 && $num_patterns < 40000 perl "--workers 5" 1 raxmlng__scheduler_mainpr5 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 39999 && $num_patterns < 100000 perl "threads_per_process=128\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainpr5workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 39999 && $num_patterns < 100000 perl "--workers 2" 1 raxmlng__scheduler_mainpr6 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 99999 perl "threads_per_process=128\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainpr6workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 99999 perl "--workers 1" 1 raxmlng__scheduler_mainbin1 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns < 10000 perl "threads_per_process=80\\n" . "mem=154G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainbin1workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns < 10000 perl "--workers 20" 1 raxmlng__scheduler_mainbin2 scheduler.conf perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 perl "threads_per_process=120\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_mainbin2workers perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 perl "--workers 10" 1 raxmlng__scheduler_othernp1 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns < 4000 perl "threads_per_process=8\\n" . "mem=15G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_othernp2 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $num_patterns < 10000 perl "threads_per_process=16\\n" . "mem=30G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_othernp3 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 9999 && $num_patterns < 60000 perl "threads_per_process=32\\n" . "mem=61G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_othernp4 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 59999 && $num_patterns < 300000 perl "threads_per_process=64\\n" . "mem=123G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_othernp5 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 perl "threads_per_process=128\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherpr1 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns < 1500 perl "threads_per_process=8\\n" . "mem=15G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherpr2 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 1499 && $num_patterns < 4000 perl "threads_per_process=16\\n" . "mem=30G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherpr3 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 3999 && $num_patterns < 10000 perl "threads_per_process=32\\n" . "mem=61G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherpr4 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 9999 && $num_patterns < 40000 perl "threads_per_process=48\\n" . "mem=92G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherpr5 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 perl "threads_per_process=128\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherbin1 scheduler.conf perl $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns < 10000 perl "threads_per_process=6\\n" . "mem=11G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherbin2 scheduler.conf perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 perl "threads_per_process=12\\n" . "mem=23G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlng__scheduler_otherall scheduler.conf perl $select_analysis eq "fb" || $select_analysis eq "I" || $select_analysis eq "rfdist" || $select_analysis eq "J" && !defined $datatype perl "threads_per_process=8\\n" . "mem=15G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 infile Sequences File (relaxed phylip format) (-s) 1 infile.txt runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) perl "runhours=$value\\n" 0.25 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. Maximum Hours to Run must be 168 or less perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on 80 processors as configured. If it runs for the entire configured time, it will consume 80 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns < 4000 The job will run on 120 processors as configured. If it runs for the entire configured time, it will consume 120 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $num_patterns < 8000 The job will run on 120 processors as configured. If it runs for the entire configured time, it will consume 120 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 7999 && $num_patterns < 40000 The job will run on 125 processors as configured. If it runs for the entire configured time, it will consume 125 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 39999 && $num_patterns < 100000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 99999 WARNING: This job will require 3,000-6,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $runtime >= 24 && $runtime < 48 WARNING: This job will require 6,000-9,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $runtime >= 48 && $runtime < 72 WARNING: This job will require 9,000-12,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $runtime >= 72 && $runtime < 96 WARNING: This job will require 12,000-15,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $runtime >= 96 && $runtime < 120 WARNING: This job will require 15,000-18,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $runtime >= 120 && $runtime < 144 WARNING: This job will require 18,000-21,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $runtime >= 144 && $runtime <= 168 The job will run on 80 processors as configured. If it runs for the entire configured time, it will consume 80 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns < 1500 The job will run on 120 processors as configured. If it runs for the entire configured time, it will consume 120 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $num_patterns < 5000 The job will run on 120 processors as configured. If it runs for the entire configured time, it will consume 120 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 4999 && $num_patterns < 10000 The job will run on 125 processors as configured. If it runs for the entire configured time, it will consume 125 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 9999 && $num_patterns < 40000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 39999 WARNING: This job will require 3,000-6,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $runtime >= 24 && $runtime < 48 WARNING: This job will require 6,000-9,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $runtime >= 48 && $runtime < 72 WARNING: This job will require 9,000-12,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $runtime >= 72 && $runtime < 96 WARNING: This job will require 12,000-15,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $runtime >= 96 && $runtime < 120 WARNING: This job will require 15,000-18,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $runtime >= 120 && $runtime < 144 WARNING: This job will require 18,000-21,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && $datatype eq "protein" && $num_patterns > 1499 && $runtime >= 144 && $runtime <= 168 The job will run on 80 processors as configured. If it runs for the entire configured time, it will consume 80 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns < 10000 The job will run on 120 processors as configured. If it runs for the entire configured time, it will consume 120 x $runtime cpu hours perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 WARNING: This job will require 3,000-6,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 && $runtime >= 24 && $runtime < 48 WARNING: This job will require 6,000-9,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 && $runtime >= 48 && $runtime < 72 WARNING: This job will require 9,000-12,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 && $runtime >= 72 && $runtime < 96 WARNING: This job will require 12,000-15,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 && $runtime >= 96 && $runtime < 120 WARNING: This job will require 15,000-18,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 && $runtime >= 120 && $runtime < 144 WARNING: This job will require 18,000-21,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl ($select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "search") && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 && $runtime >= 144 && $runtime <= 168 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns < 4000 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 3999 && $num_patterns < 10000 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 9999 && $num_patterns < 60000 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 59999 && $num_patterns < 300000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 WARNING: This job will require 3,000-6,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 && $runtime >= 24 && $runtime < 48 WARNING: This job will require 6,000-9,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 && $runtime >= 48 && $runtime < 72 WARNING: This job will require 9,000-12,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 && $runtime >= 72 && $runtime < 96 WARNING: This job will require 12,000-15,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 && $runtime >= 96 && $runtime < 120 WARNING: This job will require 15,000-18,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 && $runtime >= 120 && $runtime < 144 WARNING: This job will require 18,000-21,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype ne "protein" && $datatype ne "bin" && $datatype ne "multi" && $num_patterns > 299999 && $runtime >= 144 && $runtime <= 168 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns < 1500 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 1499 && $num_patterns < 4000 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 3999 && $num_patterns < 10000 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 $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 9999 && $num_patterns < 40000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 WARNING: This job will require 3,000-6000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 && $runtime >= 24 && $runtime < 48 WARNING: This job will require 6,000-9000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 && $runtime >= 48 && $runtime < 72 WARNING: This job will require 9,000-12000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 && $runtime >= 72 && $runtime < 96 WARNING: This job will require 12,000-15,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 && $runtime >= 96 && $runtime < 120 WARNING: This job will require 15,000-18,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 && $runtime >= 120 && $runtime < 144 WARNING: This job will require 18,000-21,000 CPU hours if it runs for the entire configured time; are you sure you want to do this? perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && $datatype eq "protein" && $num_patterns > 39999 && $runtime >= 144 && $runtime <= 168 The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x $runtime cpu hours perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns < 10000 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "all" && $select_analysis ne "bootstrap" && $select_analysis ne "search" && ($datatype eq "bin" || $datatype eq "multi") && $num_patterns > 9999 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl ($select_analysis eq "fb" || $select_analysis eq "I" || $select_analysis eq "rfdist" || $select_analysis eq "J") && !defined $datatype && !defined $num_patterns select_analysis Select the Analysis Type parse search all bootstrap evaluate fc search1 loglh fb I fA rfdist J y fJ terrace sitelh all "--all" bootstrap "--bootstrap" fc "--check" search "--search" search1 "--search1" fb "--support --tree infile.txt --bs-trees bootstraps.tre " fA "--ancestral --tree best.tre" fJ "--bsmsa" evaluate "--evaluate --tree best.tre" loglh "--loglh --tree best.tre" parse "--parse" rfdist "--rfdist --tree infile.txt" I "--bsconverge --bs-trees infile.txt" J "" y "--start" terrace "--terrace --tree best.tre" sitelh "--sitelh --tree best.tre" search To use the --ancestral option please specify a best tree perl $select_analysis eq "fA" && !defined $besttree_upload To use the --evaluate option, please specify a best ML tree perl $select_analysis eq "fe" && !defined $treetop Sorry, you cant use the --start option and provide a starting tree using -t. perl $select_analysis eq "y" && defined $treetop 20 --search is the default RAxML tree search algorithm and is substantially faster than the original search algorithm. It takes some shortcuts, but yields trees that are almost as good as the ones obtained from the full search algorithm. When --support is specified, RAxML draws the bipartitions using a bunch of topologies (typically boot-strapped trees) specified with -z onto a single tree topology specified by -t (typically the best-scoring ML tree). When --ancestral is specified, RAxML computes marginal ancestral states/sequences on a given, fixed,and rooted reference tree. If you don't know what marginal ancestral states are please read Ziheng Yang's book on Computational Molecular Evolution.. The --start option computes a randomized parsimony starting tree with RAxML and not execute an ML analysis of the tree specify --start. The program will exit after computation of the starting tree. This option can be useful if you want to assess the impact of randomized MP and Neighbor Joining starting trees on your search algorithm. They can also be used e.g. as starting trees for Derrick Zwickls GARLI program for ML inferences, which needs comparatively good starting trees to work well above approximately 500 taxa. constraint perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" Constraint tree (--tree-constraint) constraint.tre perl (defined $value) ? "--tree-constraint constraint.tre" : "" 20 This option allows you to specify an incomplete or comprehensive multifurcating constraint tree for the RAxML search in NEWICK format. Initially, multifurcations are resolved randomly. If the tree is incomplete (does not contain all taxa) the remaining taxa are added by using the MP criterion. Once a comprehensive (containing all taxa) bifurcating tree is computed, it is further optimized under ML respecting the given constraints. Important: If you specify a non-comprehensive constraint, e.g., a constraint tree that does not contain all taxa, RAxML will assume that any taxa that not found in the constraint topology are unconstrained, i.e., these taxa can be placed in any part of the tree. As an example consider an alignment with 10 taxa: Loach, Chicken, Human, Cow, Mouse, Whale, Seal, Carp, Rat, Frog. If, for example you would like Loach, Chicken, Human, Cow to be monophyletic you would specify the constraint tree as follows: ((Loach, Chicken, Human, Cow),(Mouse, Whale, Seal, Carp, Rat, Frog)); Moreover, if you would like Loach, Chicken, Human, Cow to be monophyletic and in addition Human, Cow to be monophyletic within that clade you could specify: ((Loach, Chicken, (Human, Cow)),(Mouse, Whale, Seal, Carp, Rat, Frog)); If you specify an incomplete constraint: ((Loach, Chicken, Human, Cow),(Mouse, Whale, Seal, Carp)); the two groups Loach, Chicken, Human, Cow and Mouse, Whale, Seal, Carp will be monophyletic, while Rat and Frog can end up anywhere in the tree. datatype Sequence Type perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" protein dna bin multi unphased dna num_patterns Number of patterns in your data set perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" 1000 Please specify the number of patterns in your data set. You can make a quick run to determine the correct value. perl !defined $num_patterns Knowing the number of characters in your dataset helps us determine the most efficient way to run raxml. The number of patterns is the number of unique columns in the multiple sequence alignment matrix. You can get this number from the output of the intermediate results once a job begins. Entering the number of characters per taxon in your matirx, or 1000 as the number of patterns is an ok start. Look at the intermediate results, and see if that is reasonably close. If it is not, kill the job, and adjust the number. specify_typebootstraps Use autoMRE bootstopping perl $select_analysis eq "all" || $select_analysis eq "bootstrap" 1 specify_bootstraps Specify the number of bootstraps perl $select_analysis eq "fJ" || $select_analysis eq "all" || $select_analysis eq "bootstrap" 1000 20 Please specify the number of bootstraps perl ($select_analysis eq "fJ" || $select_analysis eq "all" || $select_analysis eq "bootstrap") && !defined $specify_bootstraps Sorry, explicit bootstraps cannot exceed 500, if you need more, please use the autoMRE bootstopping option perl !$specify_typebootstraps && $specify_bootstraps > 500 specify_mrebootstraps perl $specify_typebootstraps && ($select_analysis eq "all" || $select_analysis eq "bootstrap") perl "--bs-trees autoMRE{$specify_bootstraps}" specify_nonmrebootstraps perl !$specify_typebootstraps && ($select_analysis eq "fJ" ||$select_analysis eq "all" || $select_analysis eq "bootstrap") perl "--bs-trees $specify_bootstraps" 20 specify_bscutoff Specify the bootstrap cutoff value perl $select_analysis eq "I" || $select_analysis eq "all" || $select_analysis eq "bootstrap" perl $specify_bscutoff ne $vdef ? "--bs-cutoff $specify_bscutoff":"" 0.3 Please specify the bootstrap cutoff value perl $select_analysis eq "I" && !defined $specify_bscutoff specify_bsmetric Specify the branch support metric (bs-metric) perl $select_analysis eq "fJ" ||$select_analysis eq "all" || $select_analysis eq "bootstrap" || $select_analysis eq "fb" fbp tbe fbp,tbe perl ($value ne $vdef) ? "--bs-metric $value":"" 20 fbp Specify the branch support metric perl ($select_analysis eq "fJ" ||$select_analysis eq "all" || $select_analysis eq "bootstrap") && !defined $specify_bsmetric enable_modelparamopt Enable model parameter optimization perl $select_analysis eq "evaluate" perl ($value) ? "--opt-model on":"--opt-model off" 1 20 enable_brlopt Enable branch length optimization perl $select_analysis eq "evaluate" perl ($value) ? "--opt-branches on":"--opt-branches off" 1 20 outgroup Outgroup (one or more comma-separated outgroups, see comment for syntax) perl (defined $value)? "--outgroup $value":"" 20 The correct syntax for the box is outgroup1,outgroup2,outgroupn. If white space is introduced (e.g. outgroup1, outgroup2, outgroupn) the program will fail with the message "Error, you must specify a model of substitution with the '-m' option" outprefix Prefix for Output perl defined $value ? "--prefix $value":"" 20 specify_seed Specify a value for the seed (--seed) perl defined $value ? "--seed $value":"" 20 model_opts Substitution Matrix Options dna_model perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && ($ratehet_model eq "+G" || $ratehet_model eq "+GA" || !defined $ratehet_model) && !defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable$ascl$ratehet_model$empirical" 20 dna_modelb perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && ($ratehet_model eq "+G" || $ratehet_model eq "+GA" || !defined $ratehet_model) && defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable+ASC_FELS{$ascf}$ratehet_model$empirical" 20 dna_modelc perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && ($ratehet_model eq "+G" || $ratehet_model eq "+GA" || !defined $ratehet_model) && !defined $ascf && defined $ascs perl "--model $dna_gtrcat$invariable+ASC_STAM{$ascs}$ratehet_model$empirical" 20 dna_model2 perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Gn" && !defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable$ascl+G$num_categories$empirical" 20 dna_model2b perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Gn" && defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable+ASC_FELS{$ascf}+G$num_categories$empirical" 20 dna_model2c perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Gn" && !defined $ascf && defined $ascs perl "--model $dna_gtrcat$invariable+ASC_STAM{$ascs}+G$num_categories$empirical" 20 dna_model3 perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Gna" && !defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable$ascl+G$num_categories{$specify_alpha}$empirical" 20 dna_model3b perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Gna" && defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable+ASC_FELS{$ascf}+G$num_categories{$specify_alpha}$empirical" 20 dna_model3c perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Gna" && !defined $ascf && defined $ascs perl "--model $dna_gtrcat$invariable+ASC_STAM{$ascs}+G$num_categories{$specify_alpha}$empirical" 20 dna_model4 perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Rn" && !defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable$ascl+R$num_categories$empirical" 20 dna_model4b perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Rn" && defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable+ASC_FELS{$ascf}+R$num_categories$empirical" 20 dna_model4c perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Rn" && !defined $ascf && defined $ascs perl "--model $dna_gtrcat$invariable+ASC_STAM{$ascs}+R$num_categories$empirical" 20 dna_model5 perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Rnr" && !defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable$ascl+R$num_categories{$specify_rates}{$specify_weights}$empirical" 20 dna_model5b perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Rnr" && defined $ascf && !defined $ascs perl "--model $dna_gtrcat$invariable+ASC_FELS{$ascf}+R$num_categories{$specify_rates}{$specify_weights}$empirical" 20 dna_model5c perl $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Rnr" && !defined $ascf && defined $ascs perl "--model $dna_gtrcat$invariable+ASC_STAM{$ascs}+R$num_categories{$specify_rates}{$specify_weights}$empirical" 20 dna_gtrcat Choose a nucleotide model perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $datatype eq "dna" && !defined $any_matrix_spec && !defined $partition_file JC K80 F81 HKY TN93ef TN93 K81 K81uf TPM2 TPM2uf TPM3 TPM3uf TIM1 TIM1uf TIM2 TIM2uf TIM3 TIM3uf TVMef TVM SYM GTR GTR 20 Please choose a DNA model perl $datatype eq "dna" && !defined $dna_gtrcat prot_model perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && ($ratehet_model eq "+G" || $ratehet_model eq "+GA" || !defined $ratehet_model) && !defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable$ascl$ratehet_model$empirical" 20 prot_modelb perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && ($ratehet_model eq "+G" || $ratehet_model eq "+GA" || !defined $ratehet_model) && defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_FELS{$ascf}$ratehet_model$empirical" 20 prot_modelc perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && ($ratehet_model eq "+G" || $ratehet_model eq "+GA" || !defined $ratehet_model) && !defined $ascf && defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_STAM{$ascs}$ratehet_model$empirical" 20 prot_model2 perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Gn" && !defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable$ascl+G$num_categories$empirical" 20 prot_model2b perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Gn" && defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_FELS{$ascf}+G$num_categories$empirical" 20 prot_model2c perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Gn" && !defined $ascf && defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_STAM{$ascs}+G$num_categories$empirical" 20 prot_model3 perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Gna" && !defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable$ascl+G$num_categories{$specify_alpha}$empirical" 20 prot_model3b perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Gna" && defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_FELS{$ascf}+G$num_categories{$specify_alpha}$empirical" 20 prot_model3c perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Gna" && !defined $ascf && defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_STAM{$ascs}+G$num_categories{$specify_alpha}$empirical" 20 prot_model4 perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Rn" && !defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable$ascl+R$num_categories$empirical" 20 prot_model4b perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Rn" && defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_FELS{$ascf}+R$num_categories$empirical" 20 prot_model4c perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "+Rn" && !defined $ascf && defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_STAM{$ascs}+R$num_categories$empirical" 20 prot_model5 perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Rnr" && !defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable$ascl+R$num_categories{$specify_rates}{$specify_weights}$empirical" 20 prot_model5b perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Rnr" && defined $ascf && !defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_FELS{$ascf}+R$num_categories{$specify_rates}{$specify_weights}$empirical" 20 prot_model5c perl $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file && $ratehet_model eq "Rnr" && !defined $ascf && defined $ascs perl "--model $prot_matrix_spec$invariable+ASC_STAM{$ascs}+R$num_categories{$specify_rates}{$specify_weights}$empirical" 20 prot_matrix_spec Protein Substitution Matrix perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $datatype eq "protein" && !defined $any_matrix_spec && !defined $partition_file BLOSUM62 cpREV Dayhoff DCMut DEN FLU HIVb HIVw JTT JTT-DCMut LG LG4X LG4M mtART mtMAM mtREV mtZOA PMB PROTGTR rtREV stmtREV VT WAG LG Please refer to RAxML-NG online manual for the full list of supported models: https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model bin_matrix_spec Binary Substitution Matrix (automatic, there is only one option) perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $datatype eq "bin" && !defined $any_matrix_spec && !defined $partition_file perl "--model BIN$invariable$ascl$ratehet_model$empirical" 20 For binary data there is only one choice, if this changes you can use the free text model entry option. state_value Number of states for Morphological/Multistate Model perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $datatype eq "multi" && !defined $any_matrix_spec && !defined $partition_file Morphological/multistate: MULTIx_MK, MULTIx_GTR (where x = number of states, e.g.: MULTI8_MK for a 8-state model with equal rates) state encoding multimodel_value Model for Morphological/Multistate perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $datatype eq "multi" && !defined $any_matrix_spec && !defined $partition_file _MK _GTR multi_matrix_spec Morphological/Multistate Model perl $datatype eq "multi" && !defined $any_matrix_spec && !defined $partition_file perl "--model MULTI$state_value$multimodel_value$invariable$ascl$ratehet_model$empirical" 20 unphased_value Model for Unphased diploid genotypes perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $datatype eq "unphased" && !defined $any_matrix_spec && !defined $partition_file GTJC GTHKY4 GTGTR4 GTGTR perl "--model $value$invariable$ascl$ratehet_model$empirical" 20 Unphased diploid genotypes (10 states): GTJC GTHKY4 GTGTR4 GTGTR any_matrix_spec Specify your model in free text perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && !defined $partition_file perl "--model $value" 20 You can enter any value here that is not available above. Use this for User-defined symmetries: e.g. DNA010010 (equivalent to HKY) or MULTI5_USERabcdeabcde, or for custom rates files, or for PAML files. partition_file Select a partition model file perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" perl defined $partition_file ? "--model part.txt":"" Please select a partition model file for the terrace command perl $select_analysis eq "terrace" && !defined $partition_file 20 part.txt This parameter allows you to specify a file that specifies the regions of your alignment for which an individual model of nucleotide substitution should be estimated. This will typically be used to infer trees for long (in terms of base pairs) multi-gene alignments. If DNA and protein mixed models are used together (for example) you should choose a model option based on the model of rate heterogeneity you want to use. for example: GTR+I, p3 = 181-250 Here, each line defines a partition and consist of three elements: model specification (see above) partition name range of alignment columns NOTE: In RAxML, certain model modifiers were global (e.g., GAMMA model of rate heterogeneity), and thus they were specified on the command line and not in partition file. In RAxML-NG, this limitation was lifted, i.e. it is now possible to combine partitions with and without GAMMA, proportion of invariant sites etc. (as in example above). However, this means that RAxML partition files might need to be adjusted for RAxML-NG (e.g., by adding+G for the partitions where GAMMA model of rate heterogeneity should be used). select_brlength Select branch length estimation method (--brlen) perl defined $partition_file && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && !defined $partition_file linked scaled unlinked perl ($value ne $vdef)?" -brlen $value":"" scaled 20 In case of partitioned analysis, three branch length estimation modes are available: linked - Branch lengths are identical for all partitions scaled (default) - Joint branch length estimation with individual per-partition scalers (i.e., branch lengths are proportional); unlinked - Branch lengths are estimated independently for each partition (cf. RAxML -M option) rates_file Select a custom rates file perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && !defined $partition_file 20 rates.txt If you select a file here, use the free text box to specify your model, and use the format: model{rates.txt}, for example PROTGTR{rates.txt} PAML_file Select a PAML file 20 perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && !defined $partition_file PAML.txt If you specify a file here, use the free text box to specify your PAML file, and use the format: model{PAML.txt}, for example PROTGTR{PAML.txt} character_file Specify a custom character map file perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && !defined $partition_file 20 charmap.txt If you specify a file here, use the free text box to specify +M{charmap.txt} amongsite_ratehet Among Site Rate Heterogeneity Options ratehet_model Among-site rate heterogeneity model perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" +G +GA +Gn Gna +Rn Rnr +G Please Enter a value for the number of categories perl ($ratehet_model eq "+Gn" || $ratehet_model eq "Gna" || $ratehet_model eq "+Rn"|| $ratehet_model eq "Rnr" ) && !defined $num_categories Please enter a value for alpha perl $ratehet_model eq "Gna" && !defined $specify_alpha Please enter a value for weights perl $ratehet_model eq "Rnr" && !defined $specify_weights Please enter a value for rates perl $ratehet_model eq "Rnr" && !defined $specify_rates num_categories Specify the number of categories perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && ($ratehet_model eq "+Gn" || $ratehet_model eq "Gna" || $ratehet_model eq "+Rn" || $ratehet_model eq "Rnr" ) specify_alpha Specify alpha perl $ratehet_model eq "Gna" specify_rates Specify the rates perl $ratehet_model eq "Rnr" specify_weights Specify the weights perl $ratehet_model eq "Rnr" matrix_modifiers Model Options invariable Estimate proportion of invariable sites ( + I) perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" +IO +IC userdefined_invariable Enter the user-defined proportion of invariable sites: enter {p} perl !defined $invariable && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" perl defined $value ? "+IU{$userdefined_invariable}":"" 20 This parameter adds the string +IU{p} to the command line, where p is the user defined invariable parameter. Enter the just the value of p here, and the application will place it inside the curly braces for you, eg, if you enter x the command line will print as +IU{x}. empirical Base frequencies perl $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" +FC +FO +FE +FU{freqs.txt} empirical_file Select empirical base frequencies file perl $empirical eq "+FU{freqs.txt}" freqs.txt Please select a file with empirical base frequencies perl $empirical eq "+FU{freqs.txt}" && !defined $empirical_file ascertainment_config Ascertainment Bias Confguration ascl Lewis Correction for Ascertainment bias (ASC_) perl !defined $invariable && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" +ASC_LEWIS Ascertainment bias correction will be applied only to partitions for which it is requested in the partition file (-q) perl $ascertainment eq "ASC_" && defined $partition Sorry, you can not use two types of Ascertainment bias correction perl $ascl && (defined $ascf || defined $ascs) This is useful for binary/morphological datasets that only contain variable sites (the identical morphological features are usually not included in the alignments, hence you need to correct for this, see, e.g., http://sysbio.oxfordjournals.org/content/50/6/913.short).For DNA data this option might be useful when you analyze alignments of SNPs that also don't contain constant sites. Note that, for mathematical and numerical reasons you can not apply an ascertainment bias correction to datasets or partitions that contain constantsites. In this case, RAxML will exit with an error. ascf Enter Felsenstein Correction for Ascertainment bias (ASC_) perl !defined $invariable && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" Ascertainment bias correction will be applied only to partitions for which it is requested in the partition file (-q) perl $ascertainment eq "ASC_" && defined $partition Sorry, you can not use two types of Ascertainment bias correction perl defined $ascf && defined $ascs This is useful for binary/morphological datasets that only contain variable sites (the identical morphological features are usually not included in the alignments, hence you need to correct for this, see, e.g., http://sysbio.oxfordjournals.org/content/50/6/913.short).For DNA data this option might be useful when you analyze alignments of SNPs that also don't contain constant sites. Note that, for mathematical and numerical reasons you can not apply an ascertainment bias correction to datasets or partitions that contain constantsites. In this case, RAxML will exit with an error. ascs Enter Stamatakis Correction for Ascertainment bias (ASC_) perl !defined $invariable && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" Ascertainment bias correction will be applied only to partitions for which it is requested in the partition file (-q) perl $ascertainment eq "ASC_" && defined $partition This is useful for binary/morphological datasets that only contain variable sites (the identical morphological features are usually not included in the alignments, hence you need to correct for this, see, e.g., http://sysbio.oxfordjournals.org/content/50/6/913.short).For DNA data this option might be useful when you analyze alignments of SNPs that also don't contain constant sites. Note that, for mathematical and numerical reasons you can not apply an ascertainment bias correction to datasets or partitions that contain constantsites. In this case, RAxML will exit with an error. tree_opts Tree Options besttree_upload Select a tree for terrace, or ancestral analysis perl $select_analysis eq "fA" || $select_analysis eq "terrace" best.tre Please select a tree for your terrace or ancestral analysis perl ($select_analysis eq "fA" || $select_analysis eq "terrace") && !defined $besttree_upload referencetree_upload Provide a tree to evaluate, to compute log-likelihood or to compute site likelihood perl $select_analysis eq "evaluate" || $select_analysis eq "sitelh" || $select_analysis eq "loglh" best.tre Provide a tree to evaluate, for per-site log-likelihood, or for log likelihood perl ($select_analysis eq "evaluate" || $select_analysis eq "sitelh" || $select_analysis eq "loglh") && !defined $referencetree_upload bootstrapstree_upload Select a set of bootstrap trees for support option or a posteriori analysis perl $select_analysis eq "fb" bootstraps.tre Please select a set of bootstrap trees perl ($select_analysis eq "fb") && !defined $bootstrapstree_upload starting_parstree Number of parsimony starting trees perl !$startingtree_method && !defined $constraint && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "fe" && $select_analysis ne "loglh" perl defined $value ? "--tree pars{$starting_parstree}":"" 20 RAxML-NG supports three types of starting trees. pars(imony): start from a tree generated by the parsimony-based randomized stepwise addition algorithm user-defined: load a custom starting tree from the NEWICK file. For random and parsimony, you can specify the number of trees to generate in curly brackets (e.g., pars{10} or rand{20}). In this case, RAxML-NG will perform multiple tree searches (one per each starting tree), and pick the best-scoring topology as the final ML tree. You can also combine both parsimony and random starting trees in one run, e.g. -*tree pars{10},rand{10}. starting_randtree Number of random starting trees perl !$startingtree_method && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" perl defined $value ? "--tree rand{$starting_randtree}":"" 20 rand(om): start trees from a random topology. startingtree_upload Select a custom starting tree perl !defined $constraint && $select_analysis ne "fb" && $select_analysis ne "I" && $select_analysis ne "rfdist" && $select_analysis ne "J" && $select_analysis ne "evaluate" && $select_analysis ne "loglh" perl defined $value ? " --tree startingtree.tre":"" 20 startingtree.tre Specify a user starting tree file in Newick format. Note that Newick file can also contain multiple starting trees, in which case RAxML-NG will conduct multiple tree searches (one per starting tree). consensus_opts Consensus Tree Options specify_consense Consensus type perl $select_analysis eq "J" STRICT MR MRE MR Please select a consensus type perl $select_analysis eq "J" && !defined $specify_consense 20 specify_consensethresh MR consensus threshold x (default: 50) perl $select_analysis eq "J" && $specify_consense eq "MR" 50 Consensus threshhold must be between 50 and 100. Default=50 perl $specify_consensethresh < 50 20 specify_consensethresh2 perl $select_analysis eq "J" && $specify_consense eq "MR" perl "--consense MR$specify_consensethresh --tree infile.txt" 20 specify_consensethresh3 perl $select_analysis eq "J" && $specify_consense ne "MR" perl "--consense $specify_consense --tree infile.txt" 20 setlogVerbosity Set the log verbosity (--log xxx) ERROR WARNING RESULT INFO PROGRESS VERBOSE DEBUG perl defined ($value)?" --log $value":"" 20 all_outputfiles * raxml_outputfiles RAXML_*