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Bio-BPWrapper-1.08
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/ biotree

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.

--cleanbr
--distance, -d 'node1' -d 'node2'

Prints the distance between a pair of nodes or leaves.

--delete-otus
--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'

Divides tree into number of specified segments and counts branches up to height the segment. Returns: bin_number, branch_count, bin_floor, bin_ceiling.

llt: Linear through time.

--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).

--sis-pairs
--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

CONTRIBUTORS

  • Yözen Hernández yzhernand at gmail dot com

  • Pedro Pegan

  • Weigang Qiu (Maintainer)

  • Rocky Bernstein