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Bioinformatics is the science of information handling in biology.


Field AE FTE General activities
Anders Sjölander (UPPMAX) UPPMAX Bioinformatics 100100 Bioinformatics support and training, job efficiency monitoring, project management
Björn Viklund (UPPMAX) UPPMAX Bioinformatics
100100 Bioinformatics, containers, software installs at UPPMAX
Henric Zazzi (PDC) PDC Bioinformatics 100100 Bioinformatics Application support
Martin Dahlö (UPPMAX) UPPMAX Bioinformatics 1010 Bioinformatic support


Software License Description
ABySS Free A parallel assembler for short read sequence data
ANFO Free A parallel assembler for short read sequence data
ANNOVAR Free Functional annotation of genetic variants from high-throughput sequencing data
Ab wtp Free Alignment tool for SOLiD transcript reads
BEDTools Free BEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLAST Free package for aligning nucleotide or amino acid sequences
BLAT Free an alignment tool like BLAST, but it is structured differently.
BWA Free A fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverter Free Converts bcl files to Qseq files.
BioPerl Free A community effort to produce Perl code which is useful in biology.
BioPython Free A set of freely available tools for biological computation written in Python by an international team of developers.
Bioscope Site license the pipeline stack that comes with the solid sequence platform
Bowtie Free Bowtie is an ultrafast, memory-efficient short read aligner.
CASAVA Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software
CS-Rosetta Free de novo protein structure generation
CSA Free Python implementation of the Connection-set Algebra (Djurfeldt 2012)
ClustalW Free popular multiple sequence aligner
Concaterpillar Free A hierarchical likelihood ratio test for phylogenetic congruence.
Cufflinks Free Assembles transcripts in RNA-Seq samples and calculates their abundances
Cyana Site license biological macromolecule structure calculation based on NMR conformational constraints
EMBOSS Free A free Open Source software analysis package developed for the molecular biology.
EMMAX A statistical test for large scale human or model organism association mapping accounting for the sample structure.
FASTA Free package for aligning nucleotide or amino acid sequences
FASTX Free A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
FastQC Free Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
FreeBayes Bayesian SNP and short indel caller from the Marth lab (who created Mosaik).
GARLI Performs heuristic phylogenetic searches ...
GATK Free Structured software library for writing analysis tools for next-generation sequencing data.
GCTA A tool for Genome-wide Complex Trait Analysis
GROMACS Free versatile package for molecular dynamics
HMMER Free package for working with profile hidden Markov models (HMM)
MUSIC Free C++ library for interprocess communication in large scale neuronal network simulations
Mafft Free multiple sequence alignment program
MrBayes Free Bayesian estimation of phylogeny
Muscle Free fast, high-quality multiple sequence alignment
NMRPipe Free NMR spectroscopy data analysis suite
PHYLIP Free package for inference of phylogenies
Rosetta Site license protein structure prediction suite
SAM Free hidden Markov model analysis of biological sequences
VMD Free visualise and analyse large biomolecular systems


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