BSD Portsbiology 222 DragonFly ports
Biology-related software
| Port | Version | Repository | Comment |
|---|---|---|---|
| biology/R-cran-Biobase | 2.62.0 | DPorts | Base functions for Bioconductor |
| biology/R-cran-BiocGenerics | 0.48.1 | DPorts | S4 generic functions used in Bioconductor |
| biology/R-cran-BiocManager | 1.30.25 | DPorts | Convenient tool to install and update Bioconductor packages |
| biology/ad2vcf | 0.1.6.19 | DPorts | Add allelic depth info from a SAM stream to a VCF file |
| biology/artemis | 17.0.1.11 | DPorts | DNA sequence viewer and annotation tool |
| biology/babel | 1.6_4 | DPorts | Converts among various molecular file formats |
| biology/bamtools | 2.5.2_2 | DPorts | API and toolkit for handling BAM files |
| biology/bamutil | 1.0.15 | DPorts | Utilities for working with SAM/BAM files |
| biology/barrnap | 0.9 | DPorts | BAsic Rapid Ribosomal RNA Predictor |
| biology/bbmap | 39.15 | DPorts | BBMap short read aligner, and other bioinformatic tools |
| biology/bcf-score | 1.20_1 | DPorts | Bcftools plugins for GWAS-VCF summary statistics files |
| biology/bcftools | 1.21 | DPorts | Tools for manipulating next-generation sequencing data |
| biology/bedtools | 2.31.1 | DPorts | Toolset for genome set arithmetic such as intersect, union |
| biology/bfc | g20150417 | DPorts | Correct sequencing errors from Illumina sequencing data |
| biology/bio-mocha | 1.20 | DPorts | Bcftools plugin for mosaic chromosomal alteration analysis |
| biology/bioawk | 1.0.7 | DPorts | BWK awk modified for biological data |
| biology/biolibc | 0.2.6.4 | DPorts | Low-level high-performance bioinformatics library |
| biology/biolibc-tools | 0.1.4.13_1 | DPorts | High-performance bioinformatics tools based on biolibc |
| biology/bioparser | 3.1.0 | DPorts | C++ header-only parsing library for several formats in bioinformatics |
| biology/biosig | 2.6.1_1 | DPorts | Library for reading and writing different biosignal data format |
| biology/biosoup | 0.11.0_1 | DPorts | Collection of C++ header-only data structures for bioinformatics |
| biology/bolt-lmm | 2.3.6_15 | DPorts | Mixed model association testing and variance component analysis |
| biology/bowtie | 1.3.1 | DPorts | Ultrafast, memory-efficient short read aligner |
| biology/bowtie2 | 2.5.4 | DPorts | Ultrafast, memory-efficient short read aligner |
| biology/bwa | 0.7.19 | DPorts | Burrows-Wheeler sequence aligner |
| biology/canu | 2.2_6 | DPorts | Single molecule sequence assembler |
| biology/cd-hit | 4.8.1_3 | DPorts | Clustering and comparing protein or nucleotide sequences |
| biology/cdbfasta | 2023.07.10 | DPorts | Fast indexing and retrieval of FASTA records from flat file databases |
| biology/checkm | 1.2.3_1 | DPorts | Quality assessment tool for the microbial genomes |
| biology/clustal-omega | 1.2.4 | DPorts | Multiple alignment of nucleic acid and protein, replaces clustalw |
| biology/clustalw | 2.1_3 | DPorts | Multiple alignment program for DNA or proteins |
| biology/cufflinks | 2.2.1.89_11 | DPorts | Cufflinks assembles transcripts, estimates their abundance, etc |
| biology/diamond | 2.1.9 | DPorts | BLAST-compatible local sequence aligner |
| biology/dsr-pdb | 1.0.3_15 | DPorts | Simple C++ PDB reader (reads the protein description format) |
| biology/edlib | 1.2.7 | DPorts | Fast C++ library for sequence alignment using edit distance |
| biology/emboss | 6.6.0_7 | DPorts | Collection of open source tools for genetic sequence analysis |
| biology/erminej | 3.2 | DPorts | Analyses of gene sets such as gene expression profiling studies |
| biology/exonerate | 2.4.0_1 | DPorts | Generic tool for sequence alignment |
| biology/fasda | 0.1.5_1 | DPorts | Fast and simple differential analysis |
| biology/fasta | 21.1.1_1 | DPorts | Collection of programs for searching DNA and protein databases |
| biology/fasta3 | 36.3.8_1 | DPorts | Collection of programs for searching DNA and protein databases |
| biology/fastahack | 1.0.0 | DPorts | Utility for indexing and sequence extraction from FASTA files |
| biology/fastdnaml | 1.2.2_2 | DPorts | Faster DNAML, makes phylogenetic trees using maximum likelihood |
| biology/fastool | 0.1.4 | DPorts | Simple and quick FastQ and FastA tool for file reading and conversion |
| biology/fastp | 0.23.4 | DPorts | Ultra-fast all-in-one FASTQ preprocessor |
| biology/fastqc | 0.12.1 | DPorts | Quality control tool for high throughput sequence data |
| biology/fasttree | 2.1.11 | DPorts | Approximately-maximum-likelihood phylogenetic trees from alignments |
| biology/fastx-toolkit | 0.0.14_1 | DPorts | CLI tools for Short-Reads FASTA/FASTQ files preprocessing |
| biology/fermi-lite | 0.1.13_1 | DPorts | Library and tool for assembling Illumina short reads in small regions |
| biology/figtree | 1.4.4.14 | DPorts | Graphical viewer of phylogenetic trees |
| biology/flash | 1.2.11 | DPorts | Fast Length Adjustment of SHort reads |
| biology/fluctuate | 1.40 | DPorts | Program to fit population models |
| biology/freebayes | 1.3.6_2 | DPorts | Bayesian haplotype-based polymorphism discovery and genotyping |
| biology/garlic | 1.6_1 | DPorts | Molecular viewer, editor, and visualization program |
| biology/gemma | 0.98.5_1 | DPorts | Genome-wide Efficient Mixed Model Association |
| biology/gff2ps | 0.98l | DPorts | Convert gff-formatted genomic data sets to PostScript |
| biology/gffread | 0.12.7 | DPorts | GFF/GTF format conversions, filtering, FASTA extraction, etc |
| biology/gmap | 2020.09.12 | DPorts | Genomic Mapping and Alignment Program for mRNA and EST Sequences |
| biology/gperiodic | 3.0.3_1 | DPorts | Displays a periodic table of the elements |
| biology/graphlan | 1.1.3_1 | DPorts | High-quality circular representations of taxonomic, phylogenetic trees |
| biology/hisat2 | 2.2.1_2 | DPorts | Alignment program for mapping next-generation sequencing reads |
| biology/hmmer | 3.4 | DPorts | Profile hidden Markov models for biological sequence analysis |
| biology/htslib | 1.21 | DPorts | C library for high-throughput sequencing data formats |
| biology/hyphy | 2.5.70 | DPorts | Hypothesis testing using Phylogenies |
| biology/infernal | 1.1.5 | DPorts | Search sequence databases for structural RNA homologs |
| biology/iolib | 1.14.10_1 | DPorts | General purpose trace file (and Experiment File) reading interface |
| biology/iqtree | 2.3.5 | DPorts | Efficient phylogenomic software by maximum likelihood |
| biology/jalview | 2.11.2.5 | DPorts | Viewer and editor for multiple sequence alignments |
| biology/jellyfish | 2.3.0_4 | DPorts | Fast, memory-efficient counting of k-mers in DNA |
| biology/kallisto | 0.48.0_3,1 | DPorts | Quantify abundances of transcripts from RNA-Seq data |
| biology/kmcp | 0.9.4_9 | DPorts | Accurate metagenomic profiling & fast large-scale genome searching |
| biology/lamarc | 2.1.8_1,1 | DPorts | Package of programs for computing population parameters |
| biology/libbigwig | 0.4.8 | DPorts | C library for handling bigWig files (containing genomic data) |
| biology/libcombine | 0.2.20 | DPorts | C++ library for working with the COMBINE archive format |
| biology/libgff | 2.0.0 | DPorts | GFF/GTF parsing library based on GCLib |
| biology/libgtextutils | 0.7 | DPorts | Gordon's text utilities |
| biology/libneurosim | 1.2.0_1 | DPorts | Common interfaces for neuronal simulators |
| biology/libnuml | 1.1.7 | DPorts | C++ library for Numerical Markup Language |
| biology/libsbml | 5.20.4_1 | DPorts | API Library for Working with SBML File |
| biology/libsedml | 2.0.32 | DPorts | C++ SED-ML library |
| biology/mafft | 7.267_1 | DPorts | Multiple alignment program for amino acid or nucleotide sequences |
| biology/mapm3 | 3.0_1 | DPorts | Constructs linkage maps of markers segregating in experimental crosses |
| biology/megahit | 1.2.9_1 | DPorts | Ultra-fast single-node large and complex metagenomics assembly |
| biology/migrate | 5.0.6_2 | DPorts | Program to estimate population sizes and migration rates |
| biology/minimap2 | 2.28_1 | DPorts | Pairwise aligner for genomic and spliced nucleotide sequences |
| biology/mmseqs2 | 17.b804.f | DPorts | Ultra fast and sensitive sequence search and clustering suite |
| biology/mothur | 1.48.2 | DPorts | Software for bioinformatics of the microbial ecology community |
| biology/mrbayes | 3.2.7_2 | DPorts | Bayesian inference of phylogeny |
| biology/mummer | 4.0.1 | DPorts | Modular system for rapid whole genome alignment |
| biology/muscle | 3.8.1551 | DPorts | MUltiple Sequence Comparison by Log-Expectation |
| biology/ncbi-entrez-direct | 14.9.20210423_25 | DPorts | Access to the NCBI's suite of interconnected databases |
| biology/ncbi-toolkit | 2017.01.06_9 | DPorts | NCBI development toolkit, including BLAST 2 and GenBank/Entrez support |
| biology/ngs-sdk | 3.0.1 | DPorts | Tools and libraries for using data in the INSDC Sequence Read Archives |
| biology/p5-AcePerl | 1.92_5 | DPorts | Perl5 interface to the ACEDB genome database system |
| biology/p5-Bio-ASN1-EntrezGene | 1.73_2,1 | DPorts | Regular expression-based Perl Parser for NCBI Entrez Gene |
| biology/p5-Bio-Cluster | 1.7.3_1 | DPorts | BioPerl cluster modules |
| biology/p5-Bio-Coordinate | 1.007001 | DPorts | Modules for working with biological coordinates |
| biology/p5-Bio-DB-EMBL | 1.7.4 | DPorts | Database object interface for EMBL entry retrieval |
| biology/p5-Bio-DB-NCBIHelper | 1.7.8 | DPorts | Collection of routines useful for queries to NCBI databases |
| biology/p5-Bio-Das | 1.17_4 | DPorts | Client-side library for Distributed Genome Annotation System |
| biology/p5-Bio-FeatureIO | 1.6.905 | DPorts | Handler for FeatureIO |
| biology/p5-Bio-GFF3 | 2.0_2 | DPorts | Fast low-level functions for parsing and formatting GFF3 |
| biology/p5-Bio-Glite | 0.10_2 | DPorts | Perl Interface to G-language |
| biology/p5-Bio-Graphics | 2.40_2 | DPorts | Generate GD Images of Bio::Seq Objects |
| biology/p5-Bio-MAGETAB | 1.31_2 | DPorts | Data model and utility API for the MAGE-TAB format |
| biology/p5-Bio-NEXUS | 0.78_1 | DPorts | Object-oriented Perl API for the NEXUS file format |
| biology/p5-Bio-Phylo | 2.0.1 | DPorts | Phylogenetic analysis using Perl |
| biology/p5-Bio-SCF | 1.03_2 | DPorts | Read and Update SCF Chromatographic Sequence Files |
| biology/p5-Bio-Variation | 1.7.5 | DPorts | BioPerl variation-related functionality |
| biology/p5-BioPerl | 1.007008 | DPorts | Collection of Perl modules for bioinformatics |
| biology/p5-BioPerl-Run | 1.007003 | DPorts | Wrapper modules for common bioinformatics tools |
| biology/p5-TrimGalore | 0.6.10 | DPorts | Wrapper around Cutadapt and FastQC for adapter and quality trimming |
| biology/p5-transdecoder | 5.7.1 | DPorts | Identify candidate coding regions within transcript sequences |
| biology/paml | 4.10.7 | DPorts | Phylogenetic Analysis by Maximum Likelihood (PAML) |
| biology/pbbam | 0.18.0_11 | DPorts | PacBio BAM C++ library, with SWIG bindings |
| biology/peak-classifier | 0.1.4.13_1 | DPorts | Classify ChIP/ATAC-Seq peaks based on features provided in a GFF |
| biology/pear-merger | 0.9.6_1 | DPorts | Memory-efficient and highly accurate paired-end read merger |
| biology/phyml | 3.3.20220408_1,1 | DPorts | Simple, fast, and accurate algorithm to estimate large phylogenies |
| biology/picard-tools | 2.22.9 | DPorts | CLI tools for manipulating high-throughput sequencing (HTS) data |
| biology/plink | 1.90.b6.17_5 | DPorts | Whole genome association analysis toolset |
| biology/pooler | 1.89 | DPorts | Optimise DNA sequencing primer-set combinations |
| biology/preseq | 3.2.0 | DPorts | Predict yield of distinct reads from a genomic library |
| biology/primer3 | 2.3.6 | DPorts | Primer3 helps to choose primers for PCR reactions |
| biology/prodigal | 2.6.3.16 | DPorts | Protein-coding gene prediction for prokaryotic genomes |
| biology/prodigy-lig | 1.1.3 | DPorts | Prediction of protein-small molecule binding affinities |
| biology/protomol | 2.0.3_16 | DPorts | OO, component based, framework for molecular dynamics (MD) simulations |
| biology/psi88 | 1.0_17 | DPorts | Plotting wavefunctions (molecular orbitals) in 3D |
| biology/py-Genesis-PyAPI | 1.2.1_1 | DPorts | API for the Genesis platform for genetics information processing |
| biology/py-PySCeS | 1.2.2 | DPorts | Python Simulator for Cellular Systems |
| biology/py-bcbio-gff | 0.7.1_1 | DPorts | Read and write Generic Feature Format (GFF) with Biopython integration |
| biology/py-biom-format | 2.1.16_1 | DPorts | Biological Observation Matrix (BIOM) Format Project |
| biology/py-biopython | 1.85_1 | DPorts | Collection of Python modules for bioinformatics |
| biology/py-biosig | 2.6.1_1 | DPorts | Library for reading and writing different biosignal data format |
| biology/py-bx-python | 0.13.0_1 | DPorts | Python module for reading, manipulating and writing genomic data sets |
| biology/py-crossmap | 0.7.3_1 | DPorts | Lift over genomics coordinates between assemblies |
| biology/py-cutadapt | 5.0_1 | DPorts | Trim adapters from high-throughput sequencing reads |
| biology/py-deeptools | 3.5.2_1 | DPorts | User-friendly tools for exploring deep-sequencing data |
| biology/py-deeptoolsintervals | 0.1.9_1 | DPorts | Python interface for deepTools interval trees |
| biology/py-dna-features-viewer | 3.1.3_1 | DPorts | Python library to visualize DNA features, e.g. GenBank or Gff files |
| biology/py-dnaio | 1.2.3 | DPorts | Read and write FASTQ and FASTA |
| biology/py-ete3 | 3.1.3_1 | DPorts | Framework for the analysis and visualization of trees |
| biology/py-gffutils | 0.13_1 | DPorts | Work with GFF and GTF files in a flexible database framework |
| biology/py-goatools | 1.1.6_2 | DPorts | Tools for processing and visualizing Gene Ontology terms |
| biology/py-gtfparse | 1.3.0_1 | DPorts | Parsing tools for GTF (gene transfer format) files |
| biology/py-hits | 0.1_1 | DPorts | Utilities for processing high-throughput sequencing experiments |
| biology/py-htseq | 2.0.9_1 | DPorts | Python library to facilitate programmatic analysis of sequence data |
| biology/py-libnuml | 1.1.7 | DPorts | Numerical Markup Language for Python |
| biology/py-libsedml | 2.0.32 | DPorts | SED-ML library for Python |
| biology/py-macs2 | 2.2.9.1_1 | DPorts | Identify transcription factor binding sites |
| biology/py-macs3 | 3.0.3 | DPorts | Peak caller aimed at transcription factor binding sites |
| biology/py-mrcfile | 1.5.3_1 | DPorts | MRC file I/O library which is used in structural biology |
| biology/py-newick | 1.10.0 | DPorts | Python module to read and write the Newick format |
| biology/py-ont-fast5-api | 4.0.2_1 | DPorts | Interface to HDF5 files in Oxford Nanopore .fast5 format |
| biology/py-orange3-bioinformatics | 4.8.4_1 | DPorts | Orange add-on providing common functionality for bioinformatics |
| biology/py-pandas-charm | 0.3.0_3 | DPorts | Library for getting character matrices into and out of pandas |
| biology/py-py2bit | 0.3.0_1 | DPorts | Python interface for 2bit packed nucleotide files |
| biology/py-pybigwig | 0.3.22_1 | DPorts | Python access to bigWig files using libBigWig |
| biology/py-pyfaidx | 0.5.9.5_1 | DPorts | Efficient pythonic random access to fasta subsequences |
| biology/py-pyrodigal | 3.6.3 | DPorts | Python binding for Prodigal, an ORF finder for genomes and metagenomes |
| biology/py-pysam | 0.23.0_1 | DPorts | Python module for reading, manipulating and writing genomic data sets |
| biology/py-python-libsbml | 5.20.4_1 | DPorts | LibSBML Python API |
| biology/py-pywgsim | 0.5.2_2 | DPorts | Modified wgsim genomic data simulator |
| biology/py-resdk | 21.2.1 | DPorts | Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics |
| biology/py-scikit-bio | 0.6.1 | DPorts | Data structures, algorithms, educational resources for bioinformatics |
| biology/py-valerius | 0.2_1 | DPorts | Python bioinformatics tools |
| biology/py-xenaPython | 1.0.14_1 | DPorts | API for Xena Hub to access genetic information shared through the hub |
| biology/pyfasta | 0.5.2_6 | DPorts | Fast, memory-efficient, pythonic access to fasta sequence files |
| biology/python-nexus | 2.9.0_1 | DPorts | Generic nexus file format reader for python |
| biology/rainbow | 2.0.4 | DPorts | Efficient clustering and assembling of short reads, especially for RAD |
| biology/rampler | 2.0.0_1 | DPorts | Standalone module for sampling genomic sequences |
| biology/readseq | 2.1.19 | DPorts | Read and reformat biosequences, Java command-line version |
| biology/ruby-bio | 1.5.1 | DPorts | Integrated environment for Bioinformatics written in Ruby |
| biology/rubygem-bio | 2.0.6 | DPorts | Integrated environment for Bioinformatics written in Ruby |
| biology/rubygem-bio-executables | 1.0.0 | DPorts | Collection of miscellaneous utilities for bioinformatics |
| biology/rubygem-bio-old-biofetch-emulator | 1.0.0 | DPorts | Emulate Bio::Fetch object |
| biology/rubygem-bio-shell | 1.0.1 | DPorts | Command-line interface on BioRuby |
| biology/sam2pairwise | 1.0.0 | DPorts | Show pairwise alignment for each read in a SAM file |
| biology/samtools | 1.21 | DPorts | Tools for manipulating next-generation sequencing data |
| biology/scrm | 1.7.4_1 | DPorts | Coalescent simulator for biological sequences |
| biology/seaview | 5.1,1 | DPorts | Multiple DNA/protein sequence alignment editor |
| biology/seqan | 2.4.0 | DPorts | C++ sequence analysis template library |
| biology/seqan-apps | 2.4.0_11 | DPorts | Official bioinformatic applications based on the SeqAn library |
| biology/seqan1 | 1.3.1_4 | DPorts | C++ Sequence Analysis Library |
| biology/seqkit | 2.10.0 | DPorts | Cross-platform and ultrafast toolkit for FASTA/Q file manipulation |
| biology/seqtk | 1.4 | DPorts | Tool for processing sequences in FASTA/FASTQ format |
| biology/sigviewer | 0.6.4.13_2 | DPorts | Viewing application for biosignals |
| biology/slclust | 2010.02.02 | DPorts | Single-linkage clustering with Jaccard similarity |
| biology/smithwaterman | g20160702 | DPorts | Smith-waterman-gotoh alignment algorithm |
| biology/snpeff | 5.1 | DPorts | Genetic variant annotation and effect prediction toolbox |
| biology/spoa | 4.1.0 | DPorts | C++ implementation of the partial order alignment (POA) algorithm |
| biology/sra-tools | 2.11.0_4 | DPorts | NCBI's toolkit for handling data in INSDC Sequence Read Archives |
| biology/stacks | 2.68 | DPorts | Software pipeline for building loci from short-read sequences |
| biology/star | 2.7.9.a | DPorts | Spliced Transcripts Alignment to a Reference |
| biology/stringtie | 2.1.1 | DPorts | Transcript assembly and quantification for RNA-seq |
| biology/subread | 2.1.0 | DPorts | High-performance read alignment, quantification and mutation discovery |
| biology/tRNAscan-SE | 2.0.11 | DPorts | Searching for tRNA genes in genomic sequence |
| biology/tabixpp | 1.1.2 | DPorts | C++ wrapper to tabix indexer |
| biology/taxonkit | 0.19.0 | DPorts | Practical and efficient NCBI taxonomy toolkit |
| biology/treekin | 0.5.1_7 | DPorts | Efficient computation of RNA folding dynamics |
| biology/treepuzzle | 5.2 | DPorts | Maximum likelihood phylogeny reconstruction using quartets |
| biology/trimadap | 0.1.4 | DPorts | Trim adapter sequences from Illumina data using heuristic rules |
| biology/trimmomatic | 0.39 | DPorts | Flexible read trimming tool for Illumina NGS data |
| biology/ugene | 40.1_1 | DPorts | Integrated bioinformatics toolkit |
| biology/unikmer | 0.20.0_4 | DPorts | Toolkit for nucleic acid k-mer analysis, set operations on k-mers |
| biology/vcf-split | 0.1.5.10_1 | DPorts | Split a multi-sample VCF into single-sample VCFs |
| biology/vcf2hap | 0.1.6.7_1 | DPorts | Generate .hap file from VCF for haplohseq |
| biology/vcftools | 0.1.16_2 | DPorts | Tools for working with VCF genomics files |
| biology/velvet | 1.2.10_2 | DPorts | Sequence assembler for very short reads |
| biology/viennarna | 2.7.0_1 | DPorts | Alignment tools for the structural analysis of RNA |
| biology/vt | 0.57721_3 | DPorts | Discovers short variants from Next Generation Sequencing data |
| biology/wfa2-lib | 2.3.5 | DPorts | Exact gap-affine algorithm using homology to accelerate alignment |
| biology/wise | 2.4.1_1 | DPorts | Intelligent algorithms for DNA searches |
| graphics/raster3d | 3.0.7_5 | DPorts | Set of tools for generating raster images of proteins and molecules |
| math/py-deap | 1.4.1_1 | DPorts | Distributed Evolutionary Algorithms in Python |
| science/afni | 25.0.13 | DPorts | Advanced Functional Neuro Imaging |
| science/minc2 | 2.2.00_15,1 | DPorts | Medical Imaging NetCDF |
| science/mmtf-cpp | 1.1.0_1 | DPorts | C++ MMTF format API, decoder and encoder, for molecular structures |
| science/nest | 3.8_3 | DPorts | Simulator for spiking neural network models |
| science/py-atomium | 1.0.11_3 | DPorts | Molecular modeller and file parser |
| science/py-chainer-chemistry | 0.7.1_2 | DPorts | Library for deep learning in biology and chemistry |
| science/py-pymol | 3.0.0_1 | DPorts | OpenGL-based molecular visualization system |
| science/simbody | 3.7_8 | DPorts | Multibody dynamics library for (bio)mechanical systems simulation |