Get 1000 Hours free
On the UCSD Supercomputer
Start Your TrialRelaxed neighbor joining was developed by Jason Evans, Luke Sheneman, and James Foster from the Initiative for Bioinformatics and Evolutionary STudies (IBEST) at the University of Idaho. Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ). Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
The Tool ID for this interface is CLEARCUT. It is selected with tool=CLEARCUT_
Supported parameters:
input.infile_ - Primary Input File
input.tree_file_ - Tree Input file. To use this parameter you have to manually edit your BEAUTi file. See BEAST Users mail list.
vparam.runtime_ - Float - Maximum Hours to Run (up to 168 hours) default=1.0
vparam.alignment_or_ - Switch - My data is an alignment (no =distance matrix) default=1
vparam.datatype_is_ - Excl - Datatype; DNA (default); protein.
vparam.corr_model_ - Excl - Correction Model for Computing Distance Matrix. None (default), --jukes; --kimura
vparam.use_trad_ - Switch - Use traditional Neighbor-Joining algorithm. (-N) (off).
vparam.shuff_matrix_ - Switch - Randomly shuffle the distance matrix. (-S). default=0
vparam.join_det_ - Switch - Attempt joins deterministically. (-r) ? default = 0.
vparam.spec_seed_ = Switch, Explicitly set the PRNG seed to a specific value. (-s) default=0
vparam.seed_val_ - Integer - Enter the seed value here. No default.
vparam.matrix_out_ - Switch - Output a Distance Matrix. default=0.
vparam.ntrees_out_ - Integer - Number of trees to write out. default=1
vparams.exp_dist_ - Switch - Exponential notation in distance output (-E) default=0.
vparams.exp_brl_ - Switch - Exponential notation for branch lengths (-e) default=0.