Pairwise

List::Pairwise is a Perl module with map/grep arrays and hashes pairwise. SYNOPSIS use List::Pairwise qw(:all); my %a = ( snoogy1 => 4, snoogy2 => 2, NOT => 4, snoogy3 => 5, hehe => 12, ); # keys/values emulation (only slower) my @keys = mapp {$a} %a; my @values = mapp {$b} %a;...

PairwiseTests calculates three pairwise tests to control experimentwise error rates: simple Bonferroni, Holm's sequential Bonferroni, and Benjamin & Hochberg's False Discovery Rate.

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.


Platforms: Windows, Mac, Linux

LPCforSOS is a machine learning framework with a special focus on structured output spaces and pairwise learning. It supports currently multiclass, ordinal, hierarchical, multi-label and label ranking classification settings.


Platforms: Windows, Mac, Linux

GenoDive is a Mac-only program for population genetics analyses. The present version is a beta, which means that it will still contain bugs, and some analyses are not yet fully implemented. Please report any issues, bugs or praise that you may have to the author. This version should work on Mac...


Platforms: Mac

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing...


Platforms: Mac

Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats =...


Platforms: *nix

NeoBio project consists of Bioinformatics algorithms in Java. What algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment)....


Platforms: *nix

List::MoreUtils is a Perl module that can provide the stuff missing in List::Util. SYNOPSIS use List::MoreUtils qw(any all none notall true false firstidx first_index lastidx last_index insert_after insert_after_string apply after after_incl before before_incl indexes firstval first_value...


Platforms: *nix

WordNet::Similarity::vector_pairs is a Perl module for computing semantic relatedness of word senses using second order co-occurrence vectors of glosses of the word senses. SYNOPSIS use WordNet::Similarity::vector_pairs; use WordNet::QueryData; my $wn = WordNet::QueryData->new(); my...


Platforms: *nix

Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in...


Platforms: *nix

LDhat is a C/C++ written project that was specially designed for the analysis of recombination rates from population genetic data. The following programs are included: · convert: Simple manipulation of DNA sequence data · pairwise: Parametric and nonparametric analyses of recombination ·...


Platforms: Windows

Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows...


Platforms: Windows

Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows...


Platforms: Windows

MEFIT, also known as the Microarray Experiment Functional Integration Technology is developed as a system for microarray integration. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions....


Platforms: Windows

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded...


Platforms: Mac, Linux

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of...


Platforms: Mac

HaMSTR is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes. A-priori knowledge about orthology-relationships among genes in different sets of reference species is extracted from the Inparanoid-Database....


Platforms: Mac

SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree. SEMPHY searches for both the most likely topology of the evolutionary tree, and the optimal lengths of its...


Platforms: Mac

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the...


Platforms: Mac