NAME

nextool.pl - Command-line NEXUS file manipulation tool

DESCRIPTION

Command-line Bio::NEXUS manipulation program

SYNOPSIS

nextool.pl <input_file> [output_file] [COMMAND [arguments]]

if outfile is not specified, just read input file and output to temp.nex

Commands:

    rewrite
    rename_otus <translation_file>
    reroot <outgroup_node_name> [tree_name]
    select blocks <block1 block2 ...>
    select OTU <OTU_1 OTU_2 ...> or <-f filename>
    select tree <tree_name>
    select subtree <inode_number> [tree_name] 
    select column <columns> or <-f filename>
    exclude blocks <block1 block2 ...>
    exclude OTU <otu1 otu2 ...>
    exclude subtree <inode> [treename]
    exclude column <columns> or <-f filename>
    makesets byfile <file1> [file2 file3 ...]
    makesets byinode <inode1> [inode2 inode3 ...]
    makesets byclade <OTU1> <OTU2> [OTU3 OTU4 ...]
        Square brackets are required syntax in this command:
    makesets byotus <set1>=[<OTU1 OTU2 ...>] <set2>=[<OTU3 OTU4 ...>] ...
        Square brackets are required in this command:
    makesets byunion <set1>=[<setA + setB ...>] <set2>=[<setA + setC ...>] ...
        Square brackets are required in this command:
    makesets bydifference <set1>=[<setA - setB>] <set2>=[<setA - setC>] ...
        Square brackets around 'state' argument are required in this command:
    makesets bycharstate [title=char_block_title] [set1=]"<sequence_or_intron_position>[<state>]" [set2=...]
    makesets bycladeconsensus [title=char_block_title]
    removesets <set1 set2 ...>
    listsets [set1 set2 ...]
    listsetnames
    renamesets oldname1 newname1 [oldname2 newname2 ...]

COMMANDS

rewrite

Writes the contents of <input_file> to <output_file>. This is used to standardize the format of the file. this is the default program action if <outfile> is not specified, the output file will be temp.nex

rename_otus <translation_file>

Renames OTUs (some or all) in taxa, characters and trees blocks according to translation_file. Each non-blank, non-comment (#) line of translation_file must contain oldname whitespace newname.

reroot <outgroup_node_name> [tree_name]

reroot the tree of tree_name (optional-- the first tree in trees block if not specified) with outgroup_node_name as the new outgroup

select blocks <block1 block2 ...>

Select block given in list

select OTU <OTU_1 OTU_2 ...> or <-f filename>

Selects OTUs given in list. Changes taxa block, characters block and trees block.

select tree <tree_name>

Selects one tree given the tree name. Changes taxa/characters blocks to match.

select subtree <inode_number> [tree_name]

Selects subtree given the tree name and the internal node number. Changes taxa/characters blocks to match.

select column <columns> or <-f filename>

Selects a number of columns from character lists to get a new set of character lists (for a new Bio::NEXUS file). eg, "1-3, 5 8, 10-15" (comma or space can be used to separate numbers)

exclude blocks <block1 block2 ...>

Remove blocks from file

exclude OTU <otu1 otu2 ...>

Remove OTUs from file

exclude subtree <inode> [treename]

Remove subtree rooted with 'inode' in 'treename' or the first tree if 'treename' is not specified

exclude column <columns> or <-f filename>

Remove a number of columns from character lists to get a new set of character lists (for a new Bio::NEXUS file). eg, "1-3, 5 8, 10-15" (comma or space can be used to separate numbers)

makesets byfile <file1> [file2 file3 ...]

Add sets based on OTU's listed in simple text files. Sets take names of files; OTU's should be newline-delimited in the text files.

makesets byinode <inode1> [inode2 inode3 ...]

Add sets based on ancestral internal nodes and their children

makesets byclade <OTU1> <OTU2> [OTU3 OTU4 ...]

Add sets by finding the children of the most recent common ancestor (mrca) of OTU1 and OTU2 pairs

makesets byotus <set1>=[<OTU1 OTU2 ...>] <set2>=[<OTU3 OTU4 ...>] ...

Add sets by specifying setnames and OTU's each set is to contain. Syntax is setname=[<OTU LIST>]

makesets byunion <set1>=[<setA + setB ...>] <set2>=[<setA + setC ...>] ...

Add sets by specifying setnames and which existing sets contain the OTUs the new set will comprise. Syntax is setname=[<SET LIST>]

makesets bydifference <set1>=[<setA - setB>] <set2>=[<setA - setC>] ...

Add sets by specifying setnames and which existing sets contain the OTUs that will be used in defining the new sets.

makesets bycharstate [title=char_block_title] [set1=]"<sequence_or_intron_position>[<state>]" [set2=...]

Add sets by specifying setnames and which existing sets contain the OTUs that will be used in defining the new sets.

makesets bycladeconsensus [title=char_block_title]

Add sets by finding clades that have a consensus sequence at all loci, and creating one set for each group of "otu synonyms"

removesets [-p] set1 set2 ...

Delete sets from NEXUS file. Will empty SETS Block but not remove it from file. '-p' switch allows you to specify regular expression patterns ('set\d*' will delete all sets of the form set<number>.) QUOTATION MARKS AROUND PATTERNS IS STRONGLY RECOMMENDED.

DESCRIPTION

This program provides several services in the manipulation of NEXUS files (selecting specific OTUs or tree nodes, combining files, renaming OTUs, etc.

VERSION

$Revision: 1.42 $

REQUIRES

Bio::NEXUS

AUTHOR

Chengzhi Liang <liangc@umbi.umd.edu> Peter Yang <pyang@rice.edu> Tom Hladish <hladish@umbi.umd.edu>