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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
Posted in Life Sciences
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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/
Posted in Medical Sciences
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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
Posted in Statistical
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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
Posted in Bioinformatics, Genetics
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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/
Posted in Life Sciences
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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/
Posted in Bioinformatics
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SeqPup
SeqPup is a biological sequence editor and analysis program. Find SeqPup at: http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/java/
Posted in Bioinformatics
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Populations
Population genetic software (individuals or populations distances, phylogenetic trees) Find Populations at: http://bioinformatics.org/~tryphon/populations/
Posted in Population
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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
Posted in Genetics
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PHYLIP
PHYLIP Phylogeny Inference Package computer programs for inferring phylogenies Find PHYLIP at: http://evolution.genetics.washington.edu/phylip.html
Posted in Genetics
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