Readseq 2.2 Readseq: biological sequence format interconversion utility Don Gilbert Nucleic Acid Sequence, Protein Sequence, Phylogeny / Alignment http://iubio.bio.indiana.edu/soft/molbio/readseq/java/ readseq scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=2G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 1.0 Estimate the maximum time your job will need to run (up to 72 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. Maximum Hours to Run must be between 0.1 - 72.0. perl $runtime < 0.1 || $runtime > 72.0 Please set a value for the runtime perl !defined $runtime perl "runhours=$value\\n" intiation_string perl "readseq_expanse run $" -10 infile Input sequence file perl "input.sequence" input.sequence 0 input_type Choose the Input Format perl "-inform=$value" 8 8 22 12 17 15 5 13 11 6 14 20 21 23 24 25 1 2 3 4 -9 output_type Choose the Output format perl "-f=$value" 17 8 22 12 17 15 5 13 11 6 14 18 23 24 25 1 2 3 4 -9 pretty_seqwidth Sequence Line Width perl $output_type eq "18" 60 perl " -wid=$value" -8 pretty_leftindent Left Indent perl $output_type eq "18" 2 perl " -tab=$value" -7 pretty_colspace Column space within sequence line on output 0 perl $output_type eq "18" perl " -col=$value" -6 pretty_countgap Count gap characters in sequence width 1 perl $output_type eq "18" perl ($value)? " -gap":"" -5 pretty_nameright Put sequence name on right 0 perl $output_type eq "18" perl ($value) ? " -nameright=15":"-nameleft=15" -4 pretty_indexright Put index on right 0 perl $output_type eq "18" perl ($value) ? "-nametop -numright -numtop":"-nametop -numleft -numtop" -3 pretty_interlinet How many lines between blocks 1 perl $output_type eq "18" perl " -inter=$value" -2 outputfile_nexus perl $output_type eq "17" perl " -o=outfile.nex" outfile.nex -1 outputfile_fasta perl $output_type eq "8" perl " -o=outfile.fasta" outfile.fasta -1 outputfile_clustal perl $output_type eq "22" perl " -o=outfile.aln" outfile.aln -1 outputfile_phy perl $output_type eq "12" perl " -o=outfile.phy" outfile.phy -1 outputfile_msf perl $output_type eq "15" perl " -o=outfile.msf" outfile.msf -1 outputfile_gcg perl $output_type eq "5" perl " -o=outfile.gcg" outfile.gcg -1 outputfile_xml perl $output_type eq "19" perl " -o=outfile.xml" outfile.xml -1 outputfile_plain perl $output_type eq "13" perl " -o=outfile.txt" outfile.txt -1 outputfile_phylip32 perl $output_type eq "11" perl " -o=outfile.phy" outfile.phy -1 outputfile_dnastrider perl $output_type eq "6" perl " -o=outfile.strider" outfile.strider -1 outputfile_pir_codata perl $output_type eq "14" perl " -o=outfile.pir" outfile.pir -1 outputfile_prettyprint perl $output_type eq "18" perl " -o=outfile.pretty" outfile.pretty -1 outputfile_flatfeat perl $output_type eq "23" perl " -o=outfile.fff" outfile.fff -1 outputfile_gff perl $output_type eq "24" perl " -o=outfile.gff" outfile.gff -1 outputfile_acedb perl $output_type eq "25" perl " -o=outfile.ace" outfile.ace -1 outputfile_stanford perl $output_type eq "1" perl " -o=outfile.ig" outfile.ig -1 outputfile_genbank perl $output_type eq "2" perl " -o=outfile.gb" outfile.gb -1 outputfile_nbrf perl $output_type eq "3" perl " -o=outfile.nbrf" outfile.nbrf -1 outputfile_embl perl $output_type eq "4" perl " -o=outfile.embl" outfile.embl -1 return_input *.sequence