1.3 Multiple sequence alignment using partition function posterior probabilities. Satish Chikkagoudar, Usman Roshan S. Chikkagoudar, U. Roshan and D. R. Livesay, eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities, Nucleic Acids Research, 2007. Phylogeny / Alignment http://probalign.njit.edu probalign scheduler_input scheduler.conf perl !$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 $more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=8G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) perl "runhours=$value\\n" 1.0 Maximum Hours to Run must be between 0.1 - 168.0. perl $runtime < 0.1 || $runtime > 168.0 Please set a value for the runtime perl !defined $runtime Your job will use 1 core as configured; if it runs for the entire time it will use 1 x $runtime cpu hours perl !$more_memory Your job will use 4 cores as configured; if it runs for the entire time it will use 4 x $runtime cpu hours perl $more_memory Estimate the maximum time your job will need to run (up to 168 hrs). Your job will be killed if it doesn't finish within the time you specify, however jobs with shorter maximum run times are often scheduled sooner than longer jobs. command_name perl "/expanse/projects/ngbt/opt/expanse/probalign/probalign1.4/probalign" 0 infile Input Data (multiple fasta format) perl "infile.fasta" 1 infile.fasta alignment_order Print sequences in alignment order rather than input order (-a) perl ($value) ? " -a":"" 0 7 datatype Sequence Type (Protein specifies gonnet 160; Nucleic acid specifies simple) PROTEIN Protein DNA Nucleic acid PROTEIN " -score_matrix gonnet_160" DNA " -score_matrix nuc_simple" nuc_simple 3 output_format ClustalW output format (-clustalw)? perl ($value) ? " -clustalw > outfile.aln":"> outfile.fasta" 0 10 more_memory I need more memory 0 7 dna_params Set DNA Parameters gapopenn Gap Open Penalty (-go, recommended = 4.0) perl $datatype eq "DNA" perl " -go $value" 4.0 4 Please enter a value for Gap Open penalty (recommended = 4) perl !defined $gapopenn Gap Open penalty must be positive perl $value < 0 gapextn Gap Extension Penalty (-ge, recommended = 0.25) perl $datatype eq "DNA" perl " -ge $value" 0.25 5 Please enter a value for Gap extension penalty (recommended = 0.25) perl !defined $gapextn Gap extension penalty should be positive perl $value < 0 temp_na Temperature for Nucleic Acid (-T, recommended = 1.0) perl $datatype eq "DNA" perl " -T $value" 6 1.0 Please enter a value for Temperature (recommended = 1) perl !defined $temp_na Temperature value should be positive perl $value < 0 prot_params Set Protein Parameters gapopenp Protein Gap Open Penalty (-go, recommended = 22) perl $datatype eq "gonnet_160" perl " -go $value" 4 Please enter a value for Gap Open penalty (recommended = 22) perl !defined $gapopenp Gap Open penalty must be positive perl $value < 0 22.0 gapextp Gap Extension Penalty (-ge, recommended = 1) perl $datatype eq "PROTEIN" perl " -ge $value" 5 Please enter a value for Gap extension penalty (recommended = 1) perl !defined $gapextp Gap extension penalty should be positive perl $value < 0 1.0 temp_aa Temperature for Amino Acids (-T, recommended = 5) perl $datatype eq "PROTEIN" perl " -T $value" 6 5.0 Please enter a value for Temperature (recommended = 5) perl !defined $temp_aa Temperature value should be positive perl $value < 0 output_files *