Galaxy |

Clearcut (version 1.39.5.0)

Distance Matrix:

fasta - Alignment Fasta:

seed - Set the PRNG seed to a specific value:

ntrees - the number of output trees you want clearcut to generate (default 1):

norandom - Attempt joins deterministically:

shuffle - Randomly shuffle the distance matrix:

neighbor - Use traditional Neighbor-Joining algorithm:

expblen - Use exponential notation for branch lengths:

expdist - Use exponential notation for distance:

matrixout - Generate a Distance Matrix:

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The clearcut command runs clearcut

The clearcut command allows mothur users to run the clearcut program from within mothur. The clearcut program written by 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.

v.1.20.0: Trivial upgrade to Mothur 1.33