0.91b Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis - run on XSEDE Jose Castresana Talavera, G., and Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56, 564-577. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552. Phylogeny / Alignment gblocks_xsede gblocks_invoke perl "" 0 number_nodes perl !$more_memory 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\n" . "mem=2G\\n" . "threads_per_process=1\\n" infile Input File (AFA format) perl "input.fasta" 1 input.fasta all_results * runtime 1 Maximum Hours to Run (up to 168 hours) scheduler.conf 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 1 processors as configured. If it runs for the entire configured time, it will consume $runtime cpu hours perl $runtime ne 0 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. datatype Type of sequence (-t) DNA DNA CODON Codon PROTEIN Protein DNA "-t=d" CODON "-t=c" PROTEIN "-t=p" Please choose a sequence type perl !defined $datatype 2 specify_fileextens Specify a file extension (-e) perl ($value ne $vdef) ? "-e=$value":"" -gb 30 num_seqconserved Minimum Number Of Sequences For A Conserved Position (-b1) perl (defined $value) ? "-b1=$value":"" 4 This can be any integer bigger than half the number of sequences and smaller or equal than the total number of sequences specify_cutoff Minimum Number Of Sequences For A Flank Position (-b2) perl (defined $value) ? "-b2=$value":"" 6 The number of sequences for a flank position must be greater than or equal to the minimum number of sequences for a conserved position perl defined $value && $specify_cutoff < $num_seqconserved Any integer equal or bigger than Minimum Number Of Sequences For A Conserved Position max_contignonconvserved Maximum Number Of Contiguous Nonconserved Positions (-b3) perl ($max_contignonconvserved != $vdef) ? " -b3=$value ":"" 8 8 min_blocklength Minimum Length Of A Block (-b4) perl ($min_blocklength != $vdef) ? "-b4=$value":"" 10 10 The minimum length of a block must be 2 or greater perl defined $min_blocklength && $min_blocklength < 2 specify_allowedgaps Allowed Gap Positions (-b5) perl $value ne $vdef ? "-b5=$value":"" n None h With Half a All n 12 use_similarity Use Similarity Matrices (Protein only; -b6) perl $datatype eq "PROTEIN" perl ($value) ? "-b6=y":"" 1 14 min_initialblock Minimum Length Of An Initial Block (-b0) perl (defined $value) ? "-b0=$value":"" 16 The minimum length of the initial block must be 2 or greater perl defined $min_initialblock && $min_initialblock < 2 This will be the same as the minimum length of a block by default specify_selectedblocks Selected Blocks (-s) perl ($value) ? "-s=y":"" 1 18 specify_nonconservedblocks Nonconserved Blocks (-n) perl $specify_nonconservedblocks ? "-n=y":"" 0 20 specify_ungapped Ungapped Alignment (-u) perl ($specify_ungapped) ? "-u=y":"" 0 22 specify_maskfile Selected Blocks (-k) perl ($specify_maskfile) ? "-k=y":"" 0 24 specify_resultsfile Results And Parameters File (-p) y Yes t Text s Short Text n No perl "-p=$value " y 26 configure_resultsfile Characters Per Line In Results And Parameters File (-v) perl ($configure_resultsfile != $vdef) ? " -v=$value ":"" 60 28 The minimum characters per Line in results and parameters file is 50 perl defined $configure_resultsfile && $configure_resultsfile < 50 specify_postscriptfile Postscript File With The Selected Blocks (-d) perl $specify_postscriptfile ? "-d=y":"" 0 30