Clearcut

Clearcut

Relaxed 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.  

INPUT= aligned fasta format or distance matrix: 

Test input file (aligned fasta format): clearcut_in.txt

Test output matrix file (analyzed data summary): clearcut_matrixout.txt

Test output tree file (Newick format): clearcut_outtree.tre

If you use Clearcut, please cite:

Evans, J., Sheneman, L., Foster, J.A., (2006) Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method, Journal of Molecular Evolution, 62:785-792. [pdf]

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