Statalign 3.4 Bayesian Tree Inference using both Substitution and Indel information �d�m Nov�k, Istv�n Mikl�s, Rune Lyngs�, Jotun Hein Nov�k, �., Mikl�s, I., Lyngs�, R., et al. (2008) StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics 24, 2403-2404 10.1093/bioinformatics/btn457 Phylogeny / Alignment statalign_access statalign_invoke perl !$num_chains perl "" 0 statalign_invoke2 perl $num_chains perl "" 0 scheduler_input scheduler.conf perl !$num_chains && !$more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=2G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" scheduler_input2 scheduler.conf perl !$num_chains && $more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=8G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" scheduler_input3 scheduler.conf perl $num_chains && !$more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=2G\\n" . "node_exclusive=0\\n" . "threads_per_process=2\\n" scheduler_input4 scheduler.conf perl $num_chains && $more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=8G\\n" . "node_exclusive=0\\n" . "threads_per_process=2\\n" seqfile1 Alignment File 1 perl "infile.txt" 1 infile.txt runtime Maximum Hours to Run (click here for help setting this correctly) scheduler.conf perl "runhours=$value\\n" 1.0 Maximum Hours to Run must be between 0.1 - 168 perl $runtime < 0.1 || $runtime > 168.0 Please set a value for the runtime perl !defined $runtime The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 x $runtime cpu hours perl !$num_chains && !$more_memory The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 2 x $runtime cpu hours perl !$num_chains && $more_memory The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 2 x $runtime cpu hours perl $num_chains && !$more_memory 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_chains && $more_memory Estimate the maximum time your job will need to run (up to 168 hrs). Your job will be killed if it doesn't finish within the time you specify, however jobs with shorter maximum run times are often scheduled sooner than longer jobs. num_chains Run 2 chains more_memory I need more memory seqfile2 Alignment File 2 perl "infile2.txt" 1 infile2.txt seqfile3 Alignment File 3 perl "infile3.txt" 1 infile3.txt seqfile4 Alignment File 4 perl "infile4.txt" 1 infile4.txt treefile Select a treefile (optional) perl "treefile.tre" 2 treefile.tre specify_treeuse How to use the tree? perl defined $treefile I T E I perl "-usetree=$value" 4 specify_model Select a model Jones Kimura3 RtREV MtMam Tamura92 JukesCantor Dayhoff Wag TamuraNei Felsenstein84 Felsenstein81 HKY85 Blosum CpRev ReversibleNucleotide Vt MtREV perl "-subst=$specify_model" 5 Please specify a model perl !defined $specify_model configure_mcmc perl defined $specify_burnin && !defined $randomisationperiod perl "-mcmc=$specify_burnin,$specify_cycles,$specify_rate" 6 configure_mcmc perl defined $specify_burnin && defined $randomisationPeriod perl "-mcmc=$specify_burnin,$specify_cycles,$specify_rate,$specify_randomisationperiod" 6 specify_burnin Specify the burnin 20k These options set MCMC parameters: burn-in, cycles after burn-in, sampling rate, and (optionally) initial randomisation period. The abbreviations k and m mean 1e3 and 1e6 factors. Default: 20k,50k,100,0 specify_cycles Specify the number of cycles 50k specify_rate Specify the rate 100 specify_randomisationperiod Specify the Randomisation period automate_one perl $automate_burn && !$automate_rate && !$automate_cycle perl "-automate=burn" 8 automate_two perl !$automate_burn && $automate_rate && !$automate_cycle perl "-automate=rate" 8 automate_three perl !$automate_burn && !$automate_rate && $automate_cycle perl "-automate=cycl" 8 automate_four perl $automate_burn && !$automate_rate && $automate_cycle perl "-automate=burn,cycl" 8 automate_five perl $automate_burn && $automate_rate && !$automate_cycle perl "-automate=burn,rate" 8 automate_six perl !$automate_burn && $automate_rate && $automate_cycle perl "-automate=rate,cycl" 8 automate_seven perl $automate_burn && $automate_rate && $automate_cycle perl "-automate=burn,rate,cycl" 8 automate_burn Automate the burnin automate_cycle Automate the cycle automate_rate Automate the rate Automate MCMC parameters: burn-in, cycles after burn-in, sampling rate. Select which parameters to automate by listing one or more of: burn, cycl, rate. specify_seedval Specify a seedvalue perl (defined $value) ? "-seed=$specify_seedval":"" 1 8 Sets the random seed (same value will reproduce same results for identical input and settings) report_burnin Report the burn-in perl ($value) ? "-reportBurnin=true":"" 10 Enables the printing of logging information during the burnin. specify_output Select the output format Fasta StatAlign Clustal Phylip Nexus perl defined $specify_output ? "-ot=$specify_output":"" Fasta 14 verbose_output Print additional information perl ($value) ? "-verbose=true":"" 12 Enables the printing of logging information during the burnin. all_outputfiles *