Clearcut 1.0.9 Fast Implementation of Relaxed Neighbor Joining Sheneman, L., Evans, J., Foster J.A. Sheneman, L., Evans, J., and Foster, J.A.. (2006) Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22(22):2823-2824. Phylogeny / Alignment clearcut clearcut_inv perl "clearcut " 0 infile Alignment or a Distance Matrix 40 infile scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" input_file_spec perl "--in=infile" 40 input_file_spec perl "--verbose" 30 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 || $runtime > 72.0 perl "runhours=$value\\n" alignment_or My data is an alignment (no =distance matrix) 1 perl ($value) ? "--alignment":"--distance" 30 datatype_is Datatype: perl $alignment_or DNA perl "--$value" DNA protein 30 corr_model Correction Model for Computing Distance Matrix perl !$alignment_or perl "$value" --jukes --kimura 30 adv_opts Advanced Options use_trad Use traditional Neighbor-Joining algorithm. (-N) 0 perl ($value) ? "--neighbor":"" 30 shuff_matrix Randomly shuffle the distance matrix. (-S) 0 perl ($value) ? "--shuffle":"" 30 join_det Attempt joins deterministically. (-r) 0 perl ($value) ? "--norandom":"" 30 spec_seed Explicitly set the PRNG seed to a specific value. (-s) 0 seed_val perl $spec_seed perl ($value) ? "--seed=$value":"" Please enter a seed value perl $spec_seed && !defined $seed_val 30 output_opts Output Options matrix_out Output a Distance Matrix perl ($value) ? "-m matrixout.txt":"" 0 30 tree_out perl "-o outtree.tre" 50 ntrees_out Number of trees to write out perl "--ntrees=$value" 1 50 exp_dist Exponential notation in distance output (-E) 0 perl "--expdist" 30 exp_brl Exponential notation for branch lengths (-e) 0 perl "--expblen " 30 all_results *