BSD Ports

All ports

PortSystemVersionComment
biology/hyphyDragonFly2.5.70biology/hyphy 2.5.70: Hypothesis testing using Phylogenies. DragonFly port maintained by [email protected].
biology/infernalDragonFly1.1.5biology/infernal 1.1.5: Search sequence databases for structural RNA homologs. DragonFly port maintained by [email protected].
biology/iolibDragonFly1.14.10_1biology/iolib 1.14.10_1: General purpose trace file (and Experiment File) reading interface. DragonFly port maintained by [email protected].
biology/iqtreeDragonFly2.3.5biology/iqtree 2.3.5: Efficient phylogenomic software by maximum likelihood. DragonFly port maintained by [email protected].
biology/jalviewDragonFly2.11.2.5biology/jalview 2.11.2.5: Viewer and editor for multiple sequence alignments. DragonFly port maintained by [email protected].
biology/jellyfishDragonFly2.3.0_4biology/jellyfish 2.3.0_4: Fast, memory-efficient counting of k-mers in DNA. DragonFly port maintained by [email protected].
biology/kallistoDragonFly0.48.0_3,1biology/kallisto 0.48.0_3,1: Quantify abundances of transcripts from RNA-Seq data. DragonFly port maintained by [email protected].
biology/kmcpDragonFly0.9.4_9biology/kmcp 0.9.4_9: Accurate metagenomic profiling & fast large-scale genome searching. DragonFly port maintained by [email protected].
biology/lamarcDragonFly2.1.8_1,1biology/lamarc 2.1.8_1,1: Package of programs for computing population parameters. DragonFly port maintained by [email protected].
biology/libbigwigDragonFly0.4.8biology/libbigwig 0.4.8: C library for handling bigWig files (containing genomic data). DragonFly port maintained by [email protected].
biology/libcombineDragonFly0.2.20biology/libcombine 0.2.20: C++ library for working with the COMBINE archive format. DragonFly port maintained by [email protected].
biology/libgffDragonFly2.0.0biology/libgff 2.0.0: GFF/GTF parsing library based on GCLib. DragonFly port maintained by [email protected].
biology/libgtextutilsDragonFly0.7biology/libgtextutils 0.7: Gordon's text utilities. DragonFly port maintained by [email protected].
biology/libneurosimDragonFly1.2.0_1biology/libneurosim 1.2.0_1: Common interfaces for neuronal simulators. DragonFly port maintained by [email protected].
biology/libnumlDragonFly1.1.7biology/libnuml 1.1.7: C++ library for Numerical Markup Language. DragonFly port maintained by [email protected].
biology/libsbmlDragonFly5.20.4_1biology/libsbml 5.20.4_1: API Library for Working with SBML File. DragonFly port maintained by [email protected].
biology/libsedmlDragonFly2.0.32biology/libsedml 2.0.32: C++ SED-ML library. DragonFly port maintained by [email protected].
biology/mafftDragonFly7.267_1biology/mafft 7.267_1: Multiple alignment program for amino acid or nucleotide sequences. DragonFly port maintained by [email protected].
biology/mapm3DragonFly3.0_1biology/mapm3 3.0_1: Constructs linkage maps of markers segregating in experimental crosses. DragonFly port maintained by [email protected].
biology/megahitDragonFly1.2.9_1biology/megahit 1.2.9_1: Ultra-fast single-node large and complex metagenomics assembly. DragonFly port maintained by [email protected].
biology/migrateDragonFly5.0.6_2biology/migrate 5.0.6_2: Program to estimate population sizes and migration rates. DragonFly port maintained by [email protected].
biology/minimap2DragonFly2.28_1biology/minimap2 2.28_1: Pairwise aligner for genomic and spliced nucleotide sequences. DragonFly port maintained by [email protected].
biology/mmseqs2DragonFly17.b804.fbiology/mmseqs2 17.b804.f: Ultra fast and sensitive sequence search and clustering suite. DragonFly port maintained by [email protected].
biology/mothurDragonFly1.48.2biology/mothur 1.48.2: Software for bioinformatics of the microbial ecology community. DragonFly port maintained by [email protected].
biology/mrbayesDragonFly3.2.7_2biology/mrbayes 3.2.7_2: Bayesian inference of phylogeny. DragonFly port maintained by [email protected].
biology/mummerDragonFly4.0.1biology/mummer 4.0.1: Modular system for rapid whole genome alignment. DragonFly port maintained by [email protected].
biology/muscleDragonFly3.8.1551biology/muscle 3.8.1551: MUltiple Sequence Comparison by Log-Expectation. DragonFly port maintained by [email protected].
biology/ncbi-entrez-directDragonFly14.9.20210423_25biology/ncbi-entrez-direct 14.9.20210423_25: Access to the NCBI's suite of interconnected databases. DragonFly port maintained by [email protected].
biology/ncbi-toolkitDragonFly2017.01.06_9biology/ncbi-toolkit 2017.01.06_9: NCBI development toolkit, including BLAST 2 and GenBank/Entrez support. DragonFly port maintained by [email protected].
biology/ngs-sdkDragonFly3.0.1biology/ngs-sdk 3.0.1: Tools and libraries for using data in the INSDC Sequence Read Archives. DragonFly port maintained by [email protected].
biology/p5-AcePerlDragonFly1.92_5biology/p5-AcePerl 1.92_5: Perl5 interface to the ACEDB genome database system. DragonFly port maintained by [email protected].
biology/p5-Bio-ASN1-EntrezGeneDragonFly1.73_2,1biology/p5-Bio-ASN1-EntrezGene 1.73_2,1: Regular expression-based Perl Parser for NCBI Entrez Gene. DragonFly port maintained by [email protected].
biology/p5-Bio-ClusterDragonFly1.7.3_1biology/p5-Bio-Cluster 1.7.3_1: BioPerl cluster modules. DragonFly port maintained by [email protected].
biology/p5-Bio-CoordinateDragonFly1.007001biology/p5-Bio-Coordinate 1.007001: Modules for working with biological coordinates. DragonFly port maintained by [email protected].
biology/p5-Bio-DB-EMBLDragonFly1.7.4biology/p5-Bio-DB-EMBL 1.7.4: Database object interface for EMBL entry retrieval. DragonFly port maintained by [email protected].
biology/p5-Bio-DB-NCBIHelperDragonFly1.7.8biology/p5-Bio-DB-NCBIHelper 1.7.8: Collection of routines useful for queries to NCBI databases. DragonFly port maintained by [email protected].
biology/p5-Bio-DasDragonFly1.17_4biology/p5-Bio-Das 1.17_4: Client-side library for Distributed Genome Annotation System. DragonFly port maintained by [email protected].
biology/p5-Bio-FeatureIODragonFly1.6.905biology/p5-Bio-FeatureIO 1.6.905: Handler for FeatureIO. DragonFly port maintained by [email protected].
biology/p5-Bio-GFF3DragonFly2.0_2biology/p5-Bio-GFF3 2.0_2: Fast low-level functions for parsing and formatting GFF3. DragonFly port maintained by [email protected].
biology/p5-Bio-GliteDragonFly0.10_2biology/p5-Bio-Glite 0.10_2: Perl Interface to G-language. DragonFly port maintained by [email protected].
biology/p5-Bio-GraphicsDragonFly2.40_2biology/p5-Bio-Graphics 2.40_2: Generate GD Images of Bio::Seq Objects. DragonFly port maintained by [email protected].
biology/p5-Bio-MAGETABDragonFly1.31_2biology/p5-Bio-MAGETAB 1.31_2: Data model and utility API for the MAGE-TAB format. DragonFly port maintained by [email protected].
biology/p5-Bio-NEXUSDragonFly0.78_1biology/p5-Bio-NEXUS 0.78_1: Object-oriented Perl API for the NEXUS file format. DragonFly port maintained by [email protected].
biology/p5-Bio-PhyloDragonFly2.0.1biology/p5-Bio-Phylo 2.0.1: Phylogenetic analysis using Perl. DragonFly port maintained by [email protected].
biology/p5-Bio-SCFDragonFly1.03_2biology/p5-Bio-SCF 1.03_2: Read and Update SCF Chromatographic Sequence Files. DragonFly port maintained by [email protected].
biology/p5-Bio-VariationDragonFly1.7.5biology/p5-Bio-Variation 1.7.5: BioPerl variation-related functionality. DragonFly port maintained by [email protected].
biology/p5-BioPerlDragonFly1.007008biology/p5-BioPerl 1.007008: Collection of Perl modules for bioinformatics. DragonFly port maintained by [email protected].
biology/p5-BioPerl-RunDragonFly1.007003biology/p5-BioPerl-Run 1.007003: Wrapper modules for common bioinformatics tools. DragonFly port maintained by [email protected].
biology/p5-TrimGaloreDragonFly0.6.10biology/p5-TrimGalore 0.6.10: Wrapper around Cutadapt and FastQC for adapter and quality trimming. DragonFly port maintained by [email protected].
biology/p5-transdecoderDragonFly5.7.1biology/p5-transdecoder 5.7.1: Identify candidate coding regions within transcript sequences. DragonFly port maintained by [email protected].
biology/pamlDragonFly4.10.7biology/paml 4.10.7: Phylogenetic Analysis by Maximum Likelihood (PAML). DragonFly port maintained by [email protected].
biology/pbbamDragonFly0.18.0_11biology/pbbam 0.18.0_11: PacBio BAM C++ library, with SWIG bindings. DragonFly port maintained by [email protected].
biology/peak-classifierDragonFly0.1.4.13_1biology/peak-classifier 0.1.4.13_1: Classify ChIP/ATAC-Seq peaks based on features provided in a GFF. DragonFly port maintained by [email protected].
biology/pear-mergerDragonFly0.9.6_1biology/pear-merger 0.9.6_1: Memory-efficient and highly accurate paired-end read merger. DragonFly port maintained by [email protected].
biology/phymlDragonFly3.3.20220408_1,1biology/phyml 3.3.20220408_1,1: Simple, fast, and accurate algorithm to estimate large phylogenies. DragonFly port maintained by [email protected].
biology/picard-toolsDragonFly2.22.9biology/picard-tools 2.22.9: CLI tools for manipulating high-throughput sequencing (HTS) data. DragonFly port maintained by [email protected].
biology/plinkDragonFly1.90.b6.17_5biology/plink 1.90.b6.17_5: Whole genome association analysis toolset. DragonFly port maintained by [email protected].
biology/poolerDragonFly1.89biology/pooler 1.89: Optimise DNA sequencing primer-set combinations. DragonFly port maintained by [email protected].
biology/preseqDragonFly3.2.0biology/preseq 3.2.0: Predict yield of distinct reads from a genomic library. DragonFly port maintained by [email protected].
biology/primer3DragonFly2.3.6biology/primer3 2.3.6: Primer3 helps to choose primers for PCR reactions. DragonFly port maintained by [email protected].
biology/prodigalDragonFly2.6.3.16biology/prodigal 2.6.3.16: Protein-coding gene prediction for prokaryotic genomes. DragonFly port maintained by [email protected].
biology/prodigy-ligDragonFly1.1.3biology/prodigy-lig 1.1.3: Prediction of protein-small molecule binding affinities. DragonFly port maintained by [email protected].
biology/protomolDragonFly2.0.3_16biology/protomol 2.0.3_16: OO, component based, framework for molecular dynamics (MD) simulations. DragonFly port maintained by [email protected].
biology/psi88DragonFly1.0_17biology/psi88 1.0_17: Plotting wavefunctions (molecular orbitals) in 3D. DragonFly port maintained by [email protected].
biology/py-Genesis-PyAPIDragonFly1.2.1_1biology/py-Genesis-PyAPI 1.2.1_1: API for the Genesis platform for genetics information processing. DragonFly port maintained by [email protected].
biology/py-PySCeSDragonFly1.2.2biology/py-PySCeS 1.2.2: Python Simulator for Cellular Systems. DragonFly port maintained by [email protected].
biology/py-bcbio-gffDragonFly0.7.1_1biology/py-bcbio-gff 0.7.1_1: Read and write Generic Feature Format (GFF) with Biopython integration. DragonFly port maintained by [email protected].
biology/py-biom-formatDragonFly2.1.16_1biology/py-biom-format 2.1.16_1: Biological Observation Matrix (BIOM) Format Project. DragonFly port maintained by [email protected].
biology/py-biopythonDragonFly1.85_1biology/py-biopython 1.85_1: Collection of Python modules for bioinformatics. DragonFly port maintained by [email protected].
biology/py-biosigDragonFly2.6.1_1biology/py-biosig 2.6.1_1: Library for reading and writing different biosignal data format. DragonFly port maintained by [email protected].
biology/py-bx-pythonDragonFly0.13.0_1biology/py-bx-python 0.13.0_1: Python module for reading, manipulating and writing genomic data sets. DragonFly port maintained by [email protected].
biology/py-crossmapDragonFly0.7.3_1biology/py-crossmap 0.7.3_1: Lift over genomics coordinates between assemblies. DragonFly port maintained by [email protected].
biology/py-cutadaptDragonFly5.0_1biology/py-cutadapt 5.0_1: Trim adapters from high-throughput sequencing reads. DragonFly port maintained by [email protected].
biology/py-deeptoolsDragonFly3.5.2_1biology/py-deeptools 3.5.2_1: User-friendly tools for exploring deep-sequencing data. DragonFly port maintained by [email protected].
biology/py-deeptoolsintervalsDragonFly0.1.9_1biology/py-deeptoolsintervals 0.1.9_1: Python interface for deepTools interval trees. DragonFly port maintained by [email protected].
biology/py-dna-features-viewerDragonFly3.1.3_1biology/py-dna-features-viewer 3.1.3_1: Python library to visualize DNA features, e.g. GenBank or Gff files. DragonFly port maintained by [email protected].
biology/py-dnaioDragonFly1.2.3biology/py-dnaio 1.2.3: Read and write FASTQ and FASTA. DragonFly port maintained by [email protected].
biology/py-ete3DragonFly3.1.3_1biology/py-ete3 3.1.3_1: Framework for the analysis and visualization of trees. DragonFly port maintained by [email protected].
biology/py-gffutilsDragonFly0.13_1biology/py-gffutils 0.13_1: Work with GFF and GTF files in a flexible database framework. DragonFly port maintained by [email protected].
biology/py-goatoolsDragonFly1.1.6_2biology/py-goatools 1.1.6_2: Tools for processing and visualizing Gene Ontology terms. DragonFly port maintained by [email protected].
biology/py-gtfparseDragonFly1.3.0_1biology/py-gtfparse 1.3.0_1: Parsing tools for GTF (gene transfer format) files. DragonFly port maintained by [email protected].
biology/py-hitsDragonFly0.1_1biology/py-hits 0.1_1: Utilities for processing high-throughput sequencing experiments. DragonFly port maintained by [email protected].
biology/py-htseqDragonFly2.0.9_1biology/py-htseq 2.0.9_1: Python library to facilitate programmatic analysis of sequence data. DragonFly port maintained by [email protected].
biology/py-libnumlDragonFly1.1.7biology/py-libnuml 1.1.7: Numerical Markup Language for Python. DragonFly port maintained by [email protected].
biology/py-libsedmlDragonFly2.0.32biology/py-libsedml 2.0.32: SED-ML library for Python. DragonFly port maintained by [email protected].
biology/py-macs2DragonFly2.2.9.1_1biology/py-macs2 2.2.9.1_1: Identify transcription factor binding sites. DragonFly port maintained by [email protected].
biology/py-macs3DragonFly3.0.3biology/py-macs3 3.0.3: Peak caller aimed at transcription factor binding sites. DragonFly port maintained by [email protected].
biology/py-mrcfileDragonFly1.5.3_1biology/py-mrcfile 1.5.3_1: MRC file I/O library which is used in structural biology. DragonFly port maintained by [email protected].
biology/py-newickDragonFly1.10.0biology/py-newick 1.10.0: Python module to read and write the Newick format. DragonFly port maintained by [email protected].
biology/py-ont-fast5-apiDragonFly4.0.2_1biology/py-ont-fast5-api 4.0.2_1: Interface to HDF5 files in Oxford Nanopore .fast5 format. DragonFly port maintained by [email protected].
biology/py-orange3-bioinformaticsDragonFly4.8.4_1biology/py-orange3-bioinformatics 4.8.4_1: Orange add-on providing common functionality for bioinformatics. DragonFly port maintained by [email protected].
biology/py-pandas-charmDragonFly0.3.0_3biology/py-pandas-charm 0.3.0_3: Library for getting character matrices into and out of pandas. DragonFly port maintained by [email protected].
biology/py-py2bitDragonFly0.3.0_1biology/py-py2bit 0.3.0_1: Python interface for 2bit packed nucleotide files. DragonFly port maintained by [email protected].
biology/py-pybigwigDragonFly0.3.22_1biology/py-pybigwig 0.3.22_1: Python access to bigWig files using libBigWig. DragonFly port maintained by [email protected].
biology/py-pyfaidxDragonFly0.5.9.5_1biology/py-pyfaidx 0.5.9.5_1: Efficient pythonic random access to fasta subsequences. DragonFly port maintained by [email protected].
biology/py-pyrodigalDragonFly3.6.3biology/py-pyrodigal 3.6.3: Python binding for Prodigal, an ORF finder for genomes and metagenomes. DragonFly port maintained by [email protected].
biology/py-pysamDragonFly0.23.0_1biology/py-pysam 0.23.0_1: Python module for reading, manipulating and writing genomic data sets. DragonFly port maintained by [email protected].
biology/py-python-libsbmlDragonFly5.20.4_1biology/py-python-libsbml 5.20.4_1: LibSBML Python API. DragonFly port maintained by [email protected].
biology/py-pywgsimDragonFly0.5.2_2biology/py-pywgsim 0.5.2_2: Modified wgsim genomic data simulator. DragonFly port maintained by [email protected].
biology/py-resdkDragonFly21.2.1biology/py-resdk 21.2.1: Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics. DragonFly port maintained by [email protected].