---
name: "clearcut"
section: "1"
platform: "linux"
package: "clearcut"
version: "1.0.9+git20211013.b799afe-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/clearcut"
---

# clearcut(1)

Relaxed Neighbor Joining

## 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