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Toolkit for statistical analysis of biological sequences
PyCogent is a software library for genomic biology. It is a fully integrated
and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.
Biological Observation Matrix (BIOM) Format Project
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.
Integrated environment for Bioinformatics written in Ruby
BioRuby project aims to implement integrated environment for
Bioinformatics by using Ruby.
Tools for manipulating next-generation sequencing data
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
Official Bioinformatic applications based on the SeqAn library
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.
This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged separately and the library
can be found at biology/seqan.
C++ Sequence Analysis Library
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.
This port includes only the library, the apps have been
moved to biology/seqan-apps. This is the last release of
the version 1 API, it is highly recommended to upgrade to
biology/seqan (version 2).
Multiple DNA or protein sequence alignment package
From the website:
T-Coffee is a multiple sequence alignment package. Given a set of sequences
(Proteins or DNA), T-Coffee generates a multiple sequence alignment.
Related publications:
- 3DCoffee: Combining Protein Sequences and Structures within Multiple
Sequence Alignments.
O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
Journal of Molecular Biology, Vol 340, pp385-395, 2004
- T-Coffee: A novel method for multiple sequence alignments. C.Notredame,
D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
pp205-217,2000
- COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
407-422,1998
Free, open-source, cross-platform bioinformatics toolkit
Unipro UGENE is multiplatform, open-source software with the main goal of
assisting molecular biologists without much expertise in bioinformatics to
manage, analyze, and visualize their data. UGENE integrates widely used
bioinformatics tools within one common user interface.
UGENE toolkit supports multiple biological data formats and allows the
retrieval of data from remote data sources. It provides visualization
modules for biological objects such as annotated genome sequences, Next
Generation Sequencing (NGS) assembly data, multiple sequence alignments,
phylogenetic trees, and 3D structures.
Distributed client for Protein Folding
Folding@home is a distributed computing project -- people from throughout
the world download and run software to band together to make one of the
largest supercomputers in the world. Every computer takes the project
closer to our goals.
Folding@home uses novel computational methods coupled to distributed
computing, to simulate problems millions of times more challenging than
previously achieved.
Protein folding is linked to disease, such as Alzheimer's, ALS,
Huntington's, Parkinson's disease, and many Cancers. Moreover, when
proteins do not fold correctly (i.e. "misfold"), there can be serious
consequences, including many well known diseases, such as Alzheimer's,
Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many
cancers and cancer-related syndromes.
Tool to calculate the impedance of transmission lines
atlc is a program designed for finding the properties (characteristic
impedance, inductance per meter, capacitance per meter, velocity
factor, electric field distribution) of any transmission line with
2 or 3 conductors (i.e. a normal line or coupler). It uses the
finite difference method to determine these properties, and can
handle any cross section.
The program atlc needs to know shape of the transmission line's
cross section. This cross section is stored in a data file, which
happens to be a Windows bitmap file. The bitmap file is read by
atlc, following which the program performs the analysis. Look in
/usr/local/share/examples/atlc for some examples.