NAME

biotree - Fasta tools based on BioPerl

SYNOPSIS

biotree [options] <tree file>

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).

--version, -V

Print current release version of bp-utils.

Usage: bioseq -V

--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.

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 BioPerl. 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.

REQUIRES

Perl 5.004, Getopt::Long, Pod::Usage, BioPerl

SEE ALSO

perl(1)

AUTHOR

Yozen Hernandez, Pedro Pagan, Weigang Qiu

cpanm Bio::BPWrapper

perl -MCPAN -e shell
install Bio::BPWrapper