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# OpenScience / Software / Life Sciences

## Jalview

Jalview is a multiple alignment editor written entirely in java. Find Jalview at: http://www.ebi.ac.uk/~michele/jalview/

Posted in Bioinformatics
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## Readseq

Read & reformat biosequences Find Readseq at: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

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## AnnHyb

AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats. The features includes format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination… Find AnnHyb at: http://bioinformatics.org/annhyb/

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## The Alkahest Initiative

Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. The goal is to produce a comprehensive package for data management and bioinformatics research which is composed of separable but interoperable … Continue reading

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## ALiBio: Algorithms Library for Bioinformatics

The goal of ALiBio is the give libraries and efficient fundamental algorithm to be used when developing applications in the bioinformatics field. Find ALiBio: Algorithms Library for Bioinformatics at: http://bioinformatics.org/ALiBio/

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## ABE

ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve. Find ABE at: http://bioinformatics.org/abe/

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## PAL: Phylogenetic Analysis Library

The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces … Continue reading

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## Genie

A program for the inference of demographic history from molecular phylogenies. It is primarily designed for the analysis of phylogenies reconstructed from highly variable viral gene sequences, but can be applied to other types of sequence data that contains a … Continue reading

## Phylogen

Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages … Continue reading

## JAligner – Java implementation of biological sequence alignment algorithms

JAligner is a Java implementation of biological sequence alignment algorithms. Presently, the package implements the pair wise alignment algorithm Smith-Waterman. The basic Dynamic Programming Smith-Waterman algorithm has been modified to support affine (open and extend) gap penalty. Also, Gotoh’s improvement … Continue reading

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