OpenScience / Software / Life Sciences



NeoBio – Bioinformatics algorithms in Java

NeoBio is a Java class library of Computational Biology Algorithms. The first version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman. Find NeoBio – Bioinformatics algorithms in Java at: http://neobio.sourceforge.net

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DoseLab

DoseLab is a set of software programs for quantitative comparison of measured and computed radiation dose distributions. It is written in the Matlab programming language and is easily extensible to more general applications in radiation physics. Find DoseLab at: http://doselab.sourceforge.net/

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ADS in ADE-4 : Spatial Data Analysis

ADS in ADE-4is a package devoted to multiscale analysis of spatial point patterns. The proposed methods are based on the analysis of inter-point distances, which necessitate the location of individuals in (x;y) coordinates within a given study area. These methods, … Continue reading

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GEOSS

Gene Expression Open Source System (GEOSS) is a complete system used to store and analyze gene expression data. It has a relational database, a web interface, and an analysis suite. There is also a repository for each user’s files, and … Continue reading

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Ensembl Genome Server

Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. Find Ensembl Genome Server at: http://www.ensembl.org/

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Wise2

Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. Find Wise2 at: http://www.sanger.ac.uk/Software/Wise2/

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Populations

Population genetic software (individuals or populations distances, phylogenetic trees) Find Populations at: http://bioinformatics.org/~tryphon/populations/

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PAML

Phylogenetic Analysis by Maximum Likelihood Find PAML at: http://abacus.gene.ucl.ac.uk/software/paml.html

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PHYLIP

PHYLIP Phylogeny Inference Package computer programs for inferring phylogenies Find PHYLIP at: http://evolution.genetics.washington.edu/phylip.html

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PomBase

An AceDB database for the fission yeast Schizosaccharomyces pombe. Find PomBase at: http://www.genedb.org/genedb/pombe/blast.jsp

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Posted in Genetics | Leave a comment