Difference between revisions of "Category:Bioinformatics"
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Revision as of 14:38, 12 March 2012
Empty strings are not accepted. Bioinformatics is the science of information handling in biology.
Experts
| Field | AE FTE | General activities | ||
|---|---|---|---|---|
| Anders Sjölander (UPPMAX) | UPPMAX | Bioinformatics | 100 | Bioinformatics support and training, job efficiency monitoring, project management |
| Björn Viklund (UPPMAX) | UPPMAX | Bioinformatics Containers | 100 | Bioinformatics, containers, software installs at UPPMAX |
| Henric Zazzi (PDC) | PDC | Bioinformatics | 100 | Bioinformatics Application support |
| Martin Dahlö (UPPMAX) | UPPMAX | Bioinformatics | 10 | Bioinformatic support |
Software
| 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 |
Pages in category "Bioinformatics"
The following 57 pages are in this category, out of 57 total.
