Clearcut(1) 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