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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).

The European Molecular Biology Open Software Suite (EMBOSS) is a comprehensive set (about 100) of open source tools for genetic sequence analysis. EMBOSS is produced by the European Molecular Biology Network (EMBnet - http://www.embnet.org/). All EMBOSS tools are all built around the same set of core libraries - AJAX and NUCLEUS - and therefore share a unified user interface, have similar "look and feel", and implement a uniform sequence addressing methodology. The various components of EMBOSS are distributed under the GPL, except the core libraries which are under the LGPL. EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. The EMBASSY packages live in the biology/embassy port.

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. Several additional analysis programs, including programs that produce local alignments, are available as part of version 2 of the FASTA package, which is available as the port biology/fasta. FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson (1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; Pearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in Molecular Biology 132:185-219. The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

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

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.

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.

The Biopython Project is an international association of developers who are providing freely available Python tools for use in areas of computational molecular biology such as bioinformatics and genomics. Biopython is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. Note that the current release is alpha quality, and not yet deemed to be stable. This port includes optional support for Biopython-CORBA, a CORBA interface built to the BioCorba standard (http://biocorba.org/).

The computer program avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research. The avida system is based on concepts similar to those employed by the tierra program developed by Tom Ray. It is a population of self-reproducing strings with a Turing-complete genetic basis subjected to Poisson-random mutations. The population adapts to the combination of an intrinsic fitness landscape (self-reproduction) and an externally imposed (extrinsic) fitness function provided by the researcher. By studying this system, one can examine evolutionary adaptation, general traits of living systems (such as self-organization), and other issues pertaining to theoretical or evolutionary biology and dynamic systems.

Version 2 of the FASTA packages contains many programs for performing sequence comparisons, producing local alignments, and other related tasks for analysing DNA and proteins. Currently, the FASTA2 suite is in maintenance mode. This package provides the analysis tools from FASTA2. The searching programs are available in version 3 of the FASTA packages, which may be found in the port biology/fasta3. FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R. Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA" Methods in Enzymology 183:63- 98). The FASTA2 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

ARIADNE is a package of two programs, ariadne and prospero, that compare protein sequences and profiles using the Smith-Waterman algorithm, and assesses statistical significance using a new accurate formula, described in Mott, 2000, "Accurate Formula for P-values of gapped local sequence and profile alignments" J. Mol Biol. 300:649-659. The sequence/profile comparison algorithms used in ARIADNE are standard, and are probably not the fastest implementations available. The novel part is the method for determining statistical significance, which will give thresholds of significance that are accurate to within 5% 95% of the time. The package is written in ANSI C. You are free to incorporate the method used for assessing statistical significance into third-party code, provided you cite the above reference. The routines for assessing significance are all in gaplib.c