---
name: "quicktree"
section: "1"
platform: "linux"
package: "quicktree"
version: "2.5-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/quicktree"
---

# quicktree(1)

transforms Stockholm alignment to PHYLIP phylogenetic tree

## NAME

quicktree - transforms Stockholm alignment to PHYLIP phylogenetic tree

## SYNOPSIS

**quicktree** \[*-options*\] *\<inputfile\>*

## DESCRIPTION

A Fatal Error occurred: No such option as '--help'.

## OPTIONS

**-in** \<m\|a\>        : input file is a distance matrix in phylip format (m)

-

  or an alignment in stockholm format\* (a, default)

**-out** \<m\|t\>       : output is a distance matrix in phylip format (m) or

-

  a tree in New Hampshire format

Advanced options : **-upgma**           : Use the UPGMA method to construct the tree

-

  (ignored for distance matrix outputs)

**-kimura**          : Use the kimura translation for pairwise distances

-

  (ignored for distance matrix inputs)

**-boot** \<n\>        : Calcuate bootstrap values with n iterations

-

  (ignored for distance matrix outputs)

**-v**               : print version and exit

\*Use sreformat, part of the HMMer package to convert your alignment to Stockholm format

A Fatal Error occurred: No such option as '--version'. Usage: quicktree \[-options\] \<inputfile\> Options: **-in** \<m\|a\>        : input file is a distance matrix in phylip format (m)

-

  or an alignment in stockholm format\* (a, default)

**-out** \<m\|t\>       : output is a distance matrix in phylip format (m) or

-

  a tree in New Hampshire format

Advanced options : **-upgma**           : Use the UPGMA method to construct the tree

-

  (ignored for distance matrix outputs)

**-kimura**          : Use the kimura translation for pairwise distances

-

  (ignored for distance matrix inputs)

**-boot** \<n\>        : Calcuate bootstrap values with n iterations

-

  (ignored for distance matrix outputs)

**-v**               : print version and exit

\*Use sreformat, part of the HMMer package to convert your alignment to Stockholm format

## SEE ALSO

The full documentation for **quicktree** is maintained as a Texinfo manual.  If the **info** and **quicktree** programs are properly installed at your site, the command

-

  **info quicktree**

should give you access to the complete manual.