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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