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;...

Explore correlations between variables with pairwise histograms plotted over grid.This function combines the functionality of hist3 (joint/bivariate/pairwise histogram) and plotmatrix (pairwise scatter plots over a grid). It allows one to visualize and quantify the correlations among many variables.

slmetric_pw.h is an m-function to compute metrics between two sets of vectors in pairwise way.Main Features:-- It supports about 20 metric types, including Euclidean distance (L2), Normalized Correlation, City-Block distance (L1), Quadratic distance, Minkowski distance, Hamming distance,...


Platforms: Matlab

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


Platforms: Mac

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

% Find pair-wise SQUARE EUCLIDEAN distance% or 'Weighted square euclidean' distance% between each point in A and B% For 2 vector a, b% Euclidean distance= d = sum((a-b).^2)% Weighted version = d = sum(wts.*(a-b).^2)% ------------------------------% Input:% A= m_by_p, m points in p-dimension% B=...


Platforms: Matlab

Heuristic method for the Traveling Salesman Problem (TSP)A number of nearest neighbour tours are generated from randomly selected starting points. Each tour is improved by 2-opt heuristics (pairwise exchange of edges) and the best result is selected.


Platforms: Matlab

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

jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website. jMOTU does the following: *reads input sequences in FASTA or NEXUS format *calculates...


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

BaseByBase is a whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly...


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 Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,...


Platforms: Windows

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,...


Platforms: Windows