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