Man page - clearcut(1)
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Manual
CLEARCUT
NAMESYNOPSIS
DESCRIPTION
GENERAL OPTIONS:
INPUT OPTIONS:
CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):
OUTPUT OPTIONS:
EXAMPLES:
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