Ports Search

This is the base class for the Bio::Phylo package. All other modules inherit from it, the methods defined here are applicable to all. Consult the manual for usage examples: Bio::Phylo::Manual.

Bio::SCF module allows you to read and update (in a restricted way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions.

Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects.

The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. Bioperl is a collection of object-oriented Perl modules created by the Bioperl Project. It forms the basis of a large number of bioinformatics and genomics applications. (For an interesting aside on "How Perl saved the Human Genome Project", see http://www.bioperl.org/wiki/How_Perl_saved_human_genome)

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.

PSI/88 Version 1.0 by W. L. Jorgensen & D. L. Severance To plot wavefunctions in three dimensions from semi-empirical and most popular ab initio basis sets. Valence semi-empirical, STO-3G, 3-21++G(*) and 6-31++G(d,p) basis sets are implemented for atoms H-Ar. On-line manual is available at this web site. You can also download the source code of psi88 from the above site as a ``psi88.tar.gz''. When you do ungzip and untar this archive, you will obtain some documents and the ``psi88.tar.Z'' file which is required at this port.