---
name: "tree_recon"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tree_recon"
---

# tree\_recon(1)

Tree reconstruction

## NAME

tree\_recon - Tree reconstruction

## SYNOPSIS

**tree\_recon** \[*OPTIONS*\] **-m** *IN.DIST*

## DESCRIPTION

Reconstruct phylogenetic tree from Phylip matrix *IN.DIST*.

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

### Input / Output:

- **-m**, **--matrix** *INPUT\_FILE*

  Name Phylip distance matrix file.  Must contain at least three species. Valid filetype is: *.dist*.

- **-o**, **--out-file** *OUTPUT\_FILE*

  Path to write output to. Valid filetypes are: *.newick* and *.dot*. Default: *tree.dot*.

### Algorithm Options:

- **-b**, **--build** *STRING*

  Tree building method. *nj*: neighbour-joining, *min*: UPGMA single linkage, *max*: UPGMA complete linkage, *avg*: UPGMA average linkage, *wavg*: UPGMA weighted average linkage.  Neighbour-joining creates an unrooted tree.  We root that tree at the least joined pair. One of *nj*, *min*, *max*, *avg*, and *wavg*. Default: *nj*.

## CONTACT AND REFERENCES

- For questions or comments, contact:

  Tobias Rausch \<rausch@embl.de\>

- SeqAn Homepage:

  http://www.seqan.de