NAME

       Clearcut - Relaxed Neighbor Joining

SYNOPSIS

       clearcut --in=<infilename> --out=<outfilename> [options]...

DESCRIPTION

   GENERAL OPTIONS:
       -h, --help
              Display this information.

       -V, --version
              Print the version of this program.

       -v, --verbose
              More output. (Default: OFF)

       -q, --quiet
              Silent operation. (Default: ON)

       -s, --seed=<seed>
              Explicitly set the PRNG seed to a specific value.

       -r, --norandom
              Attempt joins deterministically.  (Default: OFF)

       -S, --shuffle
              Randomly shuffle the distance matrix.  (Default: OFF)

       -N, --neighbor
              Use traditional Neighbor-Joining algorithm. (Default: OFF)

   INPUT OPTIONS:
       -I, --stdin
              Read input from STDIN.

       -d, --distance
              Input file is a distance matrix. (Default: ON)

       -a, --alignment
              Input file is a set of aligned sequences. (Default: OFF)

       -D, --DNA
              Input alignment are DNA sequences.

       -P, --protein
              Input alignment are protein sequences.

   CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):
       -j, --jukes
              Use Jukes-Cantor correction for computing distance matrix.

       -k, --kimura
              Use Kimura correction for distance matrix.

   OUTPUT OPTIONS:
       -O, --stdout
              Output tree to STDOUT.

       -m, --matrixout=<file> Output distance matrix to specified file.

       -n, --ntrees=<n>
              Output n trees.  (Default: 1)

       -e, --expblen
              Exponential notation for branch lengths. (Default: OFF)

       -E, --expdist
              Exponential notation in distance output. (Default: OFF)

   EXAMPLES:
       Compute tree by supplying distance matrix via stdin:

              clearcut --distance < distances.txt > treefile.tre

       Compute tree by supplying an alignment of DNA sequences from a file:

              clearcut --alignment --DNA --in=alignment.txt --out=treefile.tre