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clearcut - Online in the Cloud

Run clearcut in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command clearcut that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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