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TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.

lightweight C library that can parse John Gruber's [markdown] (http://daringfireball.net/projects/markdown/) format and convert it into several formats and can be easily extended. It also provides two usage examples: - mkd2html: markdown to xhtml conversion. - mkd2man: markdown to manpage conversion.

The Boost Python Library is a framework for interfacing Python and C++. It allows you to quickly and seamlessly expose C++ classes functions and objects to Python, and vice-versa, using no special tools -- just your C++ compiler. The Boost.Pyste code generator resides in a separate port: devel/boost-pyste

cfortran.h is an easy-to-use powerful bridge between C and FORTRAN. It provides a transparent, machine independent interface between C and FORTRAN routines and global data.

DOMC is a light weight implementation of the DOM in ANSI C as specified in the W3C Document Object Model Level 1, Level 2, and Level 2 Events recommendations.

The general purpose of this library is to provide C language procedures related to cartographic processes. Procedures for each of the processes will be strictly categorized and although they may share common subfunctions they will not intersect in scope.

AtomicParsley is a lightweight command line program for reading, parsing and setting metadata into MPEG-4 files supporting these styles of metadata: * iTunes-style metadata into .mp4, .m4a, .m4p, .m4v, .m4b files * 3gp-style assets in 3GPP, 3GPP2, MobileMP4 & derivatives * ISO copyright notices at movie & track level for MPEG-4 * uuid private user extension text & file embedding for MPEG-4

JDBM is a transactional persistence engine for Java. It aims to be for Java what GDBM is for other languages: a fast, simple persistence engine. You can use it to store a mix of objects and BLOBs, and all updates are done in a transactionally safe manner. JDBM also provides scalable data structures, such as HTree and B+Tree, to support persistence of large object collections. JDBM2 provides HashMap and TreeMap which are backed by disk storage. It is very easy and fast way to persist your data. JDBM2 also have minimal hardware requirements and is highly embeddable.

LTL is a C++ class template library for scientific computing which provides high performance via SSE3 floating point support for vector operations. Useful for array processing, image processing, FITS and ASCII I/O, and linear algebra (astronomical and scientific computing, in short). LTL provides dynamic arrays of up to 5-dimensions, subarrays and slicing, support for fixed size vectors and matrices including basic linear algebra operations, expression templates based evaluation, and I/O facilities for ascii and FITS format files. Users of the boost and blitz++ library may find the cross-pollination of these unique features to be fruitful.

FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, images, and user-convenience features such as status line help, and tooltips. Tooltips may even be used for 3D objects!