Difference between revisions of "Biology"
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|NCBI implementation of Basic Local Alignment Search Tool | |NCBI implementation of Basic Local Alignment Search Tool | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://blast.ncbi.nlm.nih.gov]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://blast.ncbi.nlm.nih.gov]] | ||
| + | |- | ||
| + | |namd | ||
| + | |Computer software for molecular dynamics simulation | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/namd/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.ks.uiuc.edu/Research/namd/]] | ||
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|ncbi-cxx-toolkit- | |ncbi-cxx-toolkit- | ||
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|Core C++ library for Pacific Biosciences tools | |Core C++ library for Pacific Biosciences tools | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/PacificBiosciences/pbcopper]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/PacificBiosciences/pbcopper]] | ||
| + | |- | ||
| + | |plinkseq | ||
| + | |Toolset for working with human genetic variation data | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/plinkseq/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://atgu.mgh.harvard.edu/plinkseq/]] | ||
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|prodigal | |prodigal | ||
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!colspan="3"| | !colspan="3"| | ||
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| − | !colspan="3"|'''Back to | + | !colspan="3"|'''Back to ''' [[image:Icon Disti GhostBSD.png|50px|link=Science and Engineering]] '''Science and Engineering''' |
| − | + | ||
|} | |} | ||
[[Category:Station]] | [[Category:Station]] | ||
Latest revision as of 14:19, 20 January 2020
Welcome to the Biology
|
| App/Package | Abstract | Addition or Link |
|---|---|---|
| CheckM | Quality assessment tool for the microbial genomes |  
|
| GroopM | Metagenomic binning suite |
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| InsightToolkit | Insight Toolkit |
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| Jellyfish | Fast, memory-efficient counting of k-mers in DNA |
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| abyss | Assembly By Short Sequences: parallel, paired-end sequence assembler |
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| afni | Advanced Functional Neuro Imaging |
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| artemis | DNA sequence viewer and annotation tool |
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| avida | Auto-adaptive genetic system designed for ALife research |
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| babel | Converts among various molecular file formats |
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| bamtools | API and toolkit for handling BAM files |
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| biococoa | Bioinformatics framework |
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| canu | Single molecule sequence assembler |
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| cycle | Calendar program for women |
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| cytoscape | Software to visualize molecular interaction networks, gene expression |
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| dDocent | Bash pipeline for RAD sequencing |
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| emboss | Collection of open source tools for genetic sequence analysis |
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| figtree | Graphical viewer of phylogenetic trees |
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| garlic | Molecular viewer, editor, and visualization program |
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| gperiodic | Displays a periodic table of the elements |
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| haplohseq | Identify regions of allelic imbalance |
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| hhsuite | Remote protein homology detection suite |
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| igv | Visualization tool for genomic datasets |
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| jalview | Viewer and editor for multiple sequence alignments |
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| kallisto | Quantify abundances of transcripts from RNA-Seq data |
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| libghemical | Support libraries of science/ghemical port |
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| mafft | Multiple alignment program for amino acid or nucleotide sequences |
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| massxpert | massXpert software for (bio)chemists |
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| minc2 | Medical Imaging NetCDF |
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| molden | Display molecular orbitals and electron densities in 2D and 3D |
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| mmtf-cpp | C++ MMTF format API, decoder and encoder, for molecular structures |
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| ncbi-blast | NCBI implementation of Basic Local Alignment Search Tool |
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| namd | Computer software for molecular dynamics simulation |
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| ncbi-cxx-toolkit- | NCBI C++ Toolkit |
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| p5-Bio-ASN1-EntrezGene | Regular expression-based Perl Parser for NCBI Entrez Gene |
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| p5-Bio-Cluster | BioPerl cluster modules |
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| p5-Bio-Coordinate | Modules for working with biological coordinates |
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| p5-Bio-DB-EMBL | Database object interface for EMBL entry retrieval |
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| p5-Bio-DB-NCBIHelper | Collection of routines useful for queries to NCBI databases |
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| p5-Bio-Das | Client-side library for Distributed Genome Annotation System |
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| p5-Bio-Das-Lite | Perl extension for the DAS (HTTP+XML) Protocol |
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| p5-Bio-FeatureIO | Handler for FeatureIO |
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| p5-Bio-GFF3 | Fast low-level functions for parsing and formatting GFF3 |
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| p5-Bio-Glite | Perl Interface to G-language |
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| p5-Bio-Graphics | Generate GD Images of Bio::Seq Objects |
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| p5-Bio-MAGETAB | Data model and utility API for the MAGE-TAB format |
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| p5-Bio-NEXUS | Object-oriented Perl API for the NEXUS file format |
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| p5-Bio-Phylo | Phylogenetic analysis using Perl |
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| p5-Bio-SCF | Read and Update SCF Chromatographic Sequence Files |
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| p5-Bio-Variation | BioPerl variation-related functionality |
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| p5-BioPerl | Collection of Perl modules for bioinformatics |
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| p5-BioPerl-Run | Wrapper modules for common bioinformatics tools |
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| p5-TrimGalore | Wrapper around Cutadapt and FastQC for adapter and quality trimming |
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| pbcopper | Core C++ library for Pacific Biosciences tools |
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| plinkseq | Toolset for working with human genetic variation data |
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| prodigal | Protein-coding gene prediction for prokaryotic genomes |
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| py27-multiqc | Aggregate bioinformatics analysis reports across samples and tools |
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| py27-pymol | OpenGL-based molecular visualization system |
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| py37-chainer-chemistry | Library for deep learning in biology and chemistry |
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| py37-multiqc | Aggregate bioinformatics analysis reports across samples and tools |
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| py37-orange3-bioinformatics | Orange add-on providing common functionality for bioinformatics |
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| py37-orange3-single-cell | Orange add-on for gene expression of single cell data |
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| pycogent | Toolkit for statistical analysis of biological sequences |
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| raster3d | Set of tools for generating raster images of proteins and molecules |
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| seqtools | Tools for visualising sequence alignments |
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| ugene | Free, open-source, cross-platform bioinformatics toolkit |
|
| If you don't find a package, you are looking for, we recommend to search the  Ports Collection. If it is there, than it is also in the GhostBSD ports.
| ||
Back to  Science and Engineering
| ||
