Man page - tree_recon(1)

Packages contains this manual

Package:  seqan-apps
apt-get install seqan-apps

Manuals in package:
• rabema_evaluate(1)
• alf(1)
• mason_materializer(1)
• pair_align(1)
• gustaf(1)
• stellar(1)
• razers3(1)
• sak(1)
• yara_indexer(1)
• mason_frag_sequencing(1)
• micro_razers(1)
• rabema_prepare_sam(1)
• insegt(1)
• rabema_build_gold_standard(1)
• splazers(1)
• seqan_tcoffee(1)
• yara_mapper(1)
• tree_recon(1)
• mason_genome(1)
• mason_methylation(1)
• razers(1)
• snp_store(1)
Documentations in package:
• seqan-apps

Manual

TREE_RECON

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Input / Output:
Algorithm Options:
CONTACT AND REFERENCES

---

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

---