Free bio phylo io software for linux

Bio::Phylo::Manual is a Perl module that contains a Bio::Phylo v.0.14 user guide.

This is the manual for Bio::Phylo. Bio::Phylo is a perl5 package for phylogenetic analysis. For installation instructions, read the README file in the root directory of the distribution. The stable URL for the most recent distribution is http://search.cpan.org/~rvosa/Bio-Phylo/

Bio::Biblio is a Bibliographic Query Service module.

SYNOPSIS

use Bio::Biblio;
my $biblio = new Bio::Biblio;

print $biblio->find (perl)->get_count . "n";

my $collection = $biblio->find (brazma, authors);
while ( $collection->has_next ) {
print $collection->get_next;
}

#The new() method can get parameters, for example:

$biblio = Bio::Biblio
(-access => soap,
-location => http://industry.ebi.ac.uk/soap/openBQS,
-destroy_on_exit => 0);

# See below for some one-liners

This is a class whose instances can access bibliographic repositories. It allows to query a bibliographic database (such as MEDLINE) and then to retrieve resulting citations from it. The citations are returned in an XML format which is native to the repository but there are also supporting modules for converting them into Perl objects.

The detailed descriptions of all query and retrieval methods are in Bio::DB::BiblioI (an interface). All those methods should be called on instances of this (Bio::Biblio) module.

The module complies (with some simplifications) with the specification described in the OpenBQS project. Its home page is at http://industry.ebi.ac.uk/openBQS. There are also links to available servers providing access to the bibliographic repositories (namely to MEDLINE).
The module also gives an access to a set of controlled vocabularies and their values. It allows to introspect bibliographic repositories and to find what citation resource types (such as journal and book articles, patents or technical reports) are provided, and what attributes they have, eventually what attribute values are allowed.

Here are some one-liners:

perl -MBio::Biblio -e print new Bio::Biblio->get_by_id ("94033980")
perl -MBio::Biblio
-e print join ("n", @{ new Bio::Biblio->find ("brazma")->get_all_ids })
perl -MBio::Biblio
-e print new Bio::Biblio->find ("Java")->find ("perl")->get_count

Bio::Map::CytoMap is a Bio::MapI compliant map implementation handling cytogenic bands.

SYNOPSIS

use Bio::Map::CytoMap;
my $map = new Bio::Map::CytoMap(-name => human1,
-species => $human);
foreach my $marker ( @markers ) { # get a list of markers somewhere
$map->add_element($marker);
}

This is the simple implementation of cytogenetic maps based on Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map.

For CytoMaps type is hard coded to be cytogeneticmap and units are set to but can be set to something else.

Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file.

SYNOPSIS

$block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose);

This is a class representing a history block in NEXUS file

METHODS

new

Title : new
Usage : block_object = new Bio::NEXUS::HistoryBlock($block_type, $commands, $verbose);
Function: Creates a new Bio::NEXUS::HistoryBlock object
Returns : Bio::NEXUS::HistoryBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)
Comments:

equals

Name : equals
Usage : $block->equals($another);
Function: compare if two Block objects are equal
Returns : boolean
Args : a Block object

rename_otus

Name : rename_otus
Usage : $nexus->rename_otus(%translation);
Function: rename all OTUs
Returns : a new nexus object with new OTU names
Args : a ref to hash based on OTU name pairs

Bio::AlignIO::msf is a Perl module with msf sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

This object can transform Bio::Align::AlignI objects to and from msf flat file databases.

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln

Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars(~,-)
Returns : L< Bio::Align::AlignI > object
Args : NONE

write_aln

Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : L< Bio::Align::AlignI > object

IO::Prompt is a Perl module to interactively prompt for user input.

SYNOPSIS

use IO::Prompt;
while( prompt "next: " ) {
print "You said $_n";
}

By default, this module exports a single function prompt. It prompts the user to enter some input, and returns an object that represents the user input.

You may specify various flags to the function to affect its behaviour; most notably, it defaults to automatically chomp the input, unless the -line flag is specified.

Two other functions are exported at request: hand_print, which simulates hand-typing to the console; and get_input, which is the lower-level function that actually prompts the user for a suitable input.

Note that this is an interim re-release. A full release with better documentation will follow in the near future. Meanwhile, please consult the examples directory from this modules CPAN distribution to better understand how to make use of this module.

Bio::Map::MappableI is an object that can be placed in a map.

SYNOPSIS

# get a Bio::Map::MappableI somehow
my $position = $element->map_position();
# these methods will be important for building sorted lists
if( $position->equals($p2) ) {
# do something
} elsif( $position->less_tha($p2) ) {}
elsif( $position->greater_than($p2) ) { }

This object handles the generic notion of an element placed on a (linear) Map. Elements can have multiple positions in a map such as is the case of Restriction enzyme cut sites on a sequence map. For exact information about an elements position in a map one must query the associate PositionI object which is accessible through the position() method.