tree_recon1
Tree reconstruction
Usage
tree_recon [OPTIONS]
-m
IN.DIST
Overview
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 <[email protected]>
- SeqAn Homepage:
-
http://www.seqan.de
History
- Debian 13 (Trixie) to Debian 10 (Buster): the text shown here
- Debian 9 (Stretch)
- Debian 8 (Jessie)
- Debian 7 (Wheezy) to Debian 6.0 (Squeeze)
--build since Debian 10 (Buster);
--help since Debian 10 (Buster);
--matrix since Debian 10 (Buster);
--out-file since Debian 10 (Buster);
--version since Debian 10 (Buster);
-b since Debian 10 (Buster);
-h since Debian 10 (Buster);
-m since Debian 10 (Buster);
-o since Debian 10 (Buster).
--outfile until Debian 7 (Wheezy);
-V until Debian 7 (Wheezy).