PAIR (Pairwise Alignment for Intertextual Relations) is a simple implementation of a [http://en.wikipedia.org/wiki/Sequence_alignment sequence alignment] algorithm for humanities text analysis designed to identify "similar passages" in large collections of texts. These may include direct quotations...

Gumm (*Generic and Useful Model Matcher*) is a tool that performs the schema alignment operation. This operation takes two schemas as input. As output, it produces an Alignment. An alignment is a set of associations between elements of the first (also called _source_) schema and elements of the seco...

This program expands a fasta alignment containing pseudonucleotids, in a cartesian-product fashion so the resulting alignment contains only real nucleotides (A, T/U, C, G). Python version 2.x is required. The source code is *NOT* compatible with Python 3.x. This project belongs to [http://www....

=Summary= Semantic role labeling (SRL) is an important module of spoken language understanding systems. This project extends the CoNLL-09 evaluation [http://ufal.mff.cuni.cz/conll2009-st/scorer.html metrics] for joint dependency parsing and SRL of text in order to be able to handle speech recogni...

GIZA++ is a statical machine translation toolkit that is used to train IBM Models 1-5 and an HMM word alignment model. This package also contains the source for the `mkcls` tool which generates the word classes necessary for training some of the alignment models. For more information on the orig...

scripts and tools to process and analyze bioinformatics data 1. BLAST parser 2. Sequence processor and translator

This project is developing a library for matching phenotype ontologies (e.g., anatomy or behavior) guided by a phylogenetic tree. The project includes code for the actual library, and a second tree for a simple Swing-based frontend. These trees will map into separate Eclipse projects (phylontal an...

visualization and analysis of DNA alignments generated by CAP3 detection and validation of polymorphic sites (SNPs and InDels)

Bioinformatics

==Pysam== Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the [http://samtools.sourceforge.net/ samtools] C-API. An alpha release (0.1.1) is available on the 'Downloads' page. See the 'INSTALL' file for instructions. The quick start guide is [http...