NAME
biotree - FASTA Bio::TreeIO tools
SYNOPSIS
biotree [options] [<tree file>]
biotree [-h
| --help
| --v
| --version
--man
]
DESCRIPTION
biotree will read a tree file and do reformating of branches and nodes.
Trees can be in any format supported by Bio::TreeIO in Bio::Perl. However, tree-manipulations has not been tested on all possible formats, so behavior may be unexpected with some.
Currently, tree-manipulations does not support multiple trees per file or the ability to read from standard input.
OPTIONS
- --help, -h
-
Print a brief help message and exits.
- --man
-
Print the manual page and exits.
- --distance, -d 'node1' -d 'node2'
-
Prints the distance between a pair of nodes or leaves.
- --input, -i 'format'
-
Input file format. Accepts newick and nhx.
- --length, -l
-
Print total branch length.
- --numOTU, -n
-
Print total number of OTUs (leaves).
- --output, -o 'format'
-
Output file format. Accepts newick, nhx, and tabtree.
- --reroot, -r 'newroot'
-
Reroot tree to specified node by creating new branch.
- --subset, -s 'node1,node2,node3'
-
Creates a tree of only the specified leaves/nodes and their descendants. Specifying a single internal node produces a subtree from that node.
- --otu, -u
-
Print leaf nodes with branch lengths.
- --lca, -A 'node1,node2,node3,...'
-
Returns ID of most recent common ancestor across provided nodes. Returns direct ancestor if single leaf/node provided.
- --labelnodes, -B
-
Prepends ID to each leaf/node label. Useful when identifying unlabed nodes, such as when using --prune.
- --distanceall, -D
-
Prints half-matrix list of distances between ALL leaves.
- --ltt, -G 'number_of_bins'
-
Linear through time. Divides tree into number of specified segments and counts branches up to height the segment. Returns: bin_number, branch_count, bin_floor, bin_ceiling.
- --lengthall, -L
-
Prints all nodes and branch lengths.
- --random, -M [sample_size]
-
Builds a tree of a random subset of the original tree's OTUs. Defults to selecting half of the original tree's nodes.
- --depth, -P 'node' [-D 'node'] [-D 'node']...
-
Prints depth to root. Accepts node names and/or IDs.
- --rmbl, -R
-
Remove branch lengths from tree.
- --allchildOTU, -U 'internal_node_id' | 'all'
-
Prints all OTU's that are descended from the given internal node. If no node is provided, a complete list of all internal nodes and their descendents is returned instead (given in the order of "walking" through the tree from the root node).
- --walk, -W 'otu'
-
Walks along the tree starting from the specified OTU and prints the total distance traveled while reaching each other OTU. Does not count any segment more than once.
Common Options
- --help, -h
-
Print a brief help message and exit.
- --man
-
Print the manual page and exit.
- --version, -V
-
Print current release version of this command and exit.
SEE ALSO
Bio::BPWrapper::TreeManipulations, the underlying Perl Module
CONTRIBUTORS
Yözen Hernández yzhernand at gmail dot com
Pedro Pegan
Weigang Qiu (Maintainer)
Rocky Bernstein