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