Bio To Bin

Convert::BinHex can extract data from Macintosh BinHex files. ALPHA WARNING: this code is currently in its Alpha release. Things may change drastically until the interface is hammered out: if you have suggestions or objections, please speak up now! SYNOPSIS Simple functions: use...

2clipboard is a service menu that copy the URL or the name of a file or directory to the clipboard. Installation: 1. extract 2clipboard.tar.gz 2. copy clip.py to bin somewhere in Your path (i.e. to ~/bin) 3. copy 2clipboard.desktop to ~/.kde/share/apps/konqueror/servicemenus or use the...

Shell over ICMP consists of two free and open source applications: one server and one client. Shell over ICMP project allows a user to connect to a remote shell daemon, by using ICMP protocol instead of classical TCP. Entirely written in Python, soicmp is a working proof-of-concept to...


Platforms: *nix

FindBin is a Perl module that can locate directory of original perl script. SYNOPSIS use FindBin; use lib "$FindBin::Bin/../lib"; or use FindBin qw($Bin); use lib "$Bin/../lib"; Locates the full path to the script bin directory to allow the use of paths relative to the bin directory....


Platforms: *nix

MQS (Minimalist Queue Services) is a minimalist queueing system in Free Software. The main purpose is to provide a set of basic methods in order to offer asynchronous messaging for program/application. Applications can use this type of services in order to store and retrieve message to...


Platforms: *nix

fwanalog is a shell script that parses and summarizes firewall logfiles. It currently (version 0.6.9) understands logs from ipf (tested with OpenBSD 2.8s and 2.9s ipf, also FreeBSD, NetBSD and Solaris 8 with ipf (+ ipfw on FreeBSD)), OpenBSD 3.x pf, Linux 2.2 ipchains, Linux 2.4 iptables, some...


Platforms: *nix

sh2log is a PTY sniffing program that captures all keystrokes and console output of physical and virtual consoles. sh2log works in userland and does not require the installation of a kernel module. Consequently, it can be run on a wide range of different UNIX platforms. It provides ready-to-use...


Platforms: *nix

Sivotra is a vocabulary trainer that takes simple text files as input. It allows one to quickly select sets of vocabularies and to change this selection in a flexible way. Sivotra makes use of the FLTK toolkit library. Alternatively, there is also a CLI version available. Binaries and...


Platforms: *nix

With so many exciting changes happening in the world of video editing, Avid ups the ante with this latest incarnation of Media Composer. In this FREE overview tutorial, Avid Master Trainer Jeff Greenberg shows you everything that’s new in MC6, and what it means to your workflow... Media...


Platforms: Mac

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...


Platforms: *nix

Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers...


Platforms: *nix

Bio::TreeIO::svggraph is a simple output format that converts a Tree object to an SVG output. SYNOPSIS use Bio::TreeIO; my $in = new Bio::TreeIO(-file => input, -format => newick); my $out = new Bio::TreeIO(-file => >output, -format => svggraph); while( my $tree = $in->next_tree ) { my...


Platforms: *nix

Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences to an existing model. Parameters: align2model (String) run (String) Run name db (Sequence) Sequences to align (-db) model_file (InFile) Model (-i) pipe:...


Platforms: *nix

Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats =...


Platforms: *nix

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;...


Platforms: *nix

Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files. SYNOPSIS use Bio::Affymetrix::CDF; # Parse the CDF file my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0}); $cdf->parse_from_file("foo.cdf"); # Find some fun facts about this chip type print...


Platforms: *nix

Bio::Graphics::Glyph::alignment is the "alignment" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is...


Platforms: *nix

Bio::OntologyIO::simplehierarchy is a base class parser for simple hierarchy-by-indentation type formats. SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv",...


Platforms: *nix

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...


Platforms: *nix

Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class). SYNOPSIS This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other...


Platforms: *nix