Sequences

Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO). SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my...

Term::ANSIScreen is a Perl module for terminal control using ANSI escape sequences. SYNOPSIS # qw/:color/ is exported by default, i.e. color() & colored() use Term::ANSIScreen qw/:color :cursor :screen :keyboard/; print setmode(1), setkey(a,b); print "40x25 mode now, with a mapped to...

LiteSQL is a C++ library that integrates C++ objects tightly to relational database and thus provides an object persistence layer. LiteSQL supports SQLite3, PostgreSQL and MySQL as backends. LiteSQL creates tables, indexes and sequences to database and upgrades schema when needed. In addition to...


Platforms: *nix

MyCGR is an Objective-Caml library and a collection of tools to use the Chaos Game Representation on DNA sequences. MyCGR can empirically check the level and power of the tests and apply them on DNA sequences. It can generalize the dinucleotide abundance profile to a CGR-based relative...


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

fl0p is a passive L7 flow fingerprinter that examines TCP/UDP/ICMP packet sequences. It can also can peek into cryptographic tunnels, can tell human beings and robots apart, and performs a couple of other infosec-related tricks. This approach differs from the techniques used by most other...


Platforms: *nix

Project VDW contains a package that generates van der Waerden sequences. Project VDW is a an attempt to further research into van der Waerden sequences. The software consists of a client that generates sequences, and a utility to generate unique starting seeds. The ultimate goal of this...


Platforms: *nix

Tk::event contains miscellaneous event facilities: define virtual events and generate events. SYNOPSIS $widget->eventAction(?arg, arg, ...?); The eventAction methods provides several facilities for dealing with window system events, such as defining virtual events and synthesizing events....


Platforms: *nix

Gimpel3D 2D/3D Stereo Conversion Software: Gimpel3D converts single images or frame sequences into stereoscopic 3D using a combination of traditional approaches and a proprietary projective 3D modeling system. The user works in true proportional 3D space where the scene can be viewed from any...


Platforms: Windows

Accent Composer lets you create accented letters with easy-to-remember two character sequences. Use it instead of typing codes on the numeric keypad or pasting from the Character Map utility. Accent Composer is not limited to accented characters. For instance, the copyright symbol, can be...


Platforms: Windows, XP, Windows Vista, 7, 7x64

ReNamer is a very powerful and flexible file renaming tool, which offers all the standard renaming procedures, including prefixes, suffixes, replacements, case changes, as well as removing contents of brackets, adding number sequences, changing file extensions, etc. For advanced users, there is a...


Platforms: Windows

Printing sequences or maps containing non-ASCII strings results in escape sequences. This function uses the not-so-commonly-known "string_escape" codec to facilitate printing such sequences for quick-viewing.


Platforms: Windows, Mac, *nix, Python, BSD Solaris

The usual approach to merging is to loop through both sequences taking the smallest from each until they are both exhausted. Python's "timsort" function detects order in underlying sequences and will run a C speed merge on the data. So, all that is involved is concatenating the sequences and...


Platforms: Windows, Mac, *nix, Python, BSD Solaris

C++ classes for the generation of low-discrepancy sequences used in numerical calculations (Halton, Sobol, Faure and Niederreiter (t,s) sequences, as well as n alpha sequences and pseudo-random number generators). Also classes for some other distributions


Platforms: Windows, Mac, Linux

OligoLocator is a simple, Java based application designed to identify the position of oligonucleotides within nucleic acid sequences with varying degrees of mismatch between the two.


Platforms: Windows

Padding variable length sequences script returns a pad function that implements tuple unpacking.


Platforms: Windows, Mac, *nix, Python, BSD Solaris

BioJava is a tool that includes objects for manipulating biological sequences and file parsers. It also features a DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic...


Platforms: Windows

This script takes multiple sequences and creates a list in which each item is constructed from items from each input sequence, and all possible combinations are created. If that description is confusing, you could look at the example in the docstring. It's a pretty simple transformation. The...


Platforms: Windows, Mac, *nix, Python, BSD Solaris

FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences.


Platforms: Mac, BSD, Linux

A database to handle voucher specimens of DNA sequences used for molecular phylogenetics.


Platforms: Windows, Mac, Linux