From SNIC Documentation
Jump to: navigation, search

Empty strings are not accepted. Bioinformatics is the science of information handling in biology.


  FieldAE FTEGeneral activities
Anders Sjölander (UPPMAX)UPPMAXBioinformatics100Bioinformatics support and training, job efficiency monitoring, project management
Björn Viklund (UPPMAX)UPPMAXBioinformatics
100Bioinformatics, containers, software installs at UPPMAX
Henric Zazzi (PDC)PDCBioinformatics100Bioinformatics Application support
Martin Dahlö (UPPMAX)UPPMAXBioinformatics10Bioinformatic support


ABySSFreeA parallel assembler for short read sequence data
ANFOFreeA parallel assembler for short read sequence data
ANNOVARFreeFunctional annotation of genetic variants from high-throughput sequencing data
Ab wtpFreeAlignment tool for SOLiD transcript reads
BEDToolsFreeBEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLASTFreepackage for aligning nucleotide or amino acid sequences
BLATFreean alignment tool like BLAST, but it is structured differently.
BWAFreeA fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverterFreeConverts bcl files to Qseq files.
BioPerlFreeA community effort to produce Perl code which is useful in biology.
BioPythonFreeA set of freely available tools for biological computation written in Python by an international team of developers.
BioscopeSite licensethe pipeline stack that comes with the solid sequence platform
BowtieFreeBowtie is an ultrafast, memory-efficient short read aligner.
CASAVAIllumina's Consensus Assessment of Sequence and Variation (CASAVA) software
CS-RosettaFreede novo protein structure generation
CSAFreePython implementation of the Connection-set Algebra (Djurfeldt 2012)
ClustalWFreepopular multiple sequence aligner
ConcaterpillarFreeA hierarchical likelihood ratio test for phylogenetic congruence.
CufflinksFreeAssembles transcripts in RNA-Seq samples and calculates their abundances
CyanaSite licensebiological macromolecule structure calculation based on NMR conformational constraints
EMBOSSFreeA free Open Source software analysis package developed for the molecular biology.
EMMAXA statistical test for large scale human or model organism association mapping accounting for the sample structure.
FASTAFreepackage for aligning nucleotide or amino acid sequences
FASTXFreeA collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
FastQCFreeAims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
FreeBayesBayesian SNP and short indel caller from the Marth lab (who created Mosaik).
GARLIPerforms heuristic phylogenetic searches ...
GATKFreeStructured software library for writing analysis tools for next-generation sequencing data.
GCTAA tool for Genome-wide Complex Trait Analysis
GROMACSFreeversatile package for molecular dynamics
HMMERFreepackage for working with profile hidden Markov models (HMM)
MUSICFreeC++ library for interprocess communication in large scale neuronal network simulations
MafftFreemultiple sequence alignment program
MrBayesFreeBayesian estimation of phylogeny
MuscleFreefast, high-quality multiple sequence alignment
NMRPipeFreeNMR spectroscopy data analysis suite
PHYLIPFreepackage for inference of phylogenies
RosettaSite licenseprotein structure prediction suite
SAMFreehidden Markov model analysis of biological sequences
VMDFreevisualise and analyse large biomolecular systems