| biology/fastahack | DragonFly | 1.0.0 | biology/fastahack 1.0.0: Utility for indexing and sequence extraction from FASTA files. DragonFly port maintained by [email protected]. |
| biology/fastdnaml | DragonFly | 1.2.2_2 | biology/fastdnaml 1.2.2_2: Faster DNAML, makes phylogenetic trees using maximum likelihood. DragonFly port maintained by [email protected]. |
| biology/fastool | DragonFly | 0.1.4 | biology/fastool 0.1.4: Simple and quick FastQ and FastA tool for file reading and conversion. DragonFly port maintained by [email protected]. |
| biology/fastp | DragonFly | 0.23.4 | biology/fastp 0.23.4: Ultra-fast all-in-one FASTQ preprocessor. DragonFly port maintained by [email protected]. |
| biology/fastqc | DragonFly | 0.12.1 | biology/fastqc 0.12.1: Quality control tool for high throughput sequence data. DragonFly port maintained by [email protected]. |
| biology/fasttree | DragonFly | 2.1.11 | biology/fasttree 2.1.11: Approximately-maximum-likelihood phylogenetic trees from alignments. DragonFly port maintained by [email protected]. |
| biology/fastx-toolkit | DragonFly | 0.0.14_1 | biology/fastx-toolkit 0.0.14_1: CLI tools for Short-Reads FASTA/FASTQ files preprocessing. DragonFly port maintained by [email protected]. |
| biology/fermi-lite | DragonFly | 0.1.13_1 | biology/fermi-lite 0.1.13_1: Library and tool for assembling Illumina short reads in small regions. DragonFly port maintained by [email protected]. |
| biology/figtree | DragonFly | 1.4.4.14 | biology/figtree 1.4.4.14: Graphical viewer of phylogenetic trees. DragonFly port maintained by [email protected]. |
| biology/flash | DragonFly | 1.2.11 | biology/flash 1.2.11: Fast Length Adjustment of SHort reads. DragonFly port maintained by [email protected]. |
| biology/fluctuate | DragonFly | 1.40 | biology/fluctuate 1.40: Program to fit population models. DragonFly port maintained by [email protected]. |
| biology/freebayes | DragonFly | 1.3.6_2 | biology/freebayes 1.3.6_2: Bayesian haplotype-based polymorphism discovery and genotyping. DragonFly port maintained by [email protected]. |
| biology/garlic | DragonFly | 1.6_1 | biology/garlic 1.6_1: Molecular viewer, editor, and visualization program. DragonFly port maintained by [email protected]. |
| biology/gemma | DragonFly | 0.98.5_1 | biology/gemma 0.98.5_1: Genome-wide Efficient Mixed Model Association. DragonFly port maintained by [email protected]. |
| biology/gff2ps | DragonFly | 0.98l | biology/gff2ps 0.98l: Convert gff-formatted genomic data sets to PostScript. DragonFly port maintained by [email protected]. |
| biology/gffread | DragonFly | 0.12.7 | biology/gffread 0.12.7: GFF/GTF format conversions, filtering, FASTA extraction, etc. DragonFly port maintained by [email protected]. |
| biology/gmap | DragonFly | 2020.09.12 | biology/gmap 2020.09.12: Genomic Mapping and Alignment Program for mRNA and EST Sequences. DragonFly port maintained by [email protected]. |
| biology/gperiodic | DragonFly | 3.0.3_1 | biology/gperiodic 3.0.3_1: Displays a periodic table of the elements. DragonFly port maintained by [email protected]. |
| biology/graphlan | DragonFly | 1.1.3_1 | biology/graphlan 1.1.3_1: High-quality circular representations of taxonomic, phylogenetic trees. DragonFly port maintained by [email protected]. |
| biology/hisat2 | DragonFly | 2.2.1_2 | biology/hisat2 2.2.1_2: Alignment program for mapping next-generation sequencing reads. DragonFly port maintained by [email protected]. |
| biology/hmmer | DragonFly | 3.4 | biology/hmmer 3.4: Profile hidden Markov models for biological sequence analysis. DragonFly port maintained by [email protected]. |
| biology/htslib | DragonFly | 1.21 | biology/htslib 1.21: C library for high-throughput sequencing data formats. DragonFly port maintained by [email protected]. |
| biology/hyphy | DragonFly | 2.5.70 | biology/hyphy 2.5.70: Hypothesis testing using Phylogenies. DragonFly port maintained by [email protected]. |
| biology/infernal | DragonFly | 1.1.5 | biology/infernal 1.1.5: Search sequence databases for structural RNA homologs. DragonFly port maintained by [email protected]. |
| biology/iolib | DragonFly | 1.14.10_1 | biology/iolib 1.14.10_1: General purpose trace file (and Experiment File) reading interface. DragonFly port maintained by [email protected]. |
| biology/iqtree | DragonFly | 2.3.5 | biology/iqtree 2.3.5: Efficient phylogenomic software by maximum likelihood. DragonFly port maintained by [email protected]. |
| biology/jalview | DragonFly | 2.11.2.5 | biology/jalview 2.11.2.5: Viewer and editor for multiple sequence alignments. DragonFly port maintained by [email protected]. |
| biology/jellyfish | DragonFly | 2.3.0_4 | biology/jellyfish 2.3.0_4: Fast, memory-efficient counting of k-mers in DNA. DragonFly port maintained by [email protected]. |
| biology/kallisto | DragonFly | 0.48.0_3,1 | biology/kallisto 0.48.0_3,1: Quantify abundances of transcripts from RNA-Seq data. DragonFly port maintained by [email protected]. |
| biology/kmcp | DragonFly | 0.9.4_9 | biology/kmcp 0.9.4_9: Accurate metagenomic profiling & fast large-scale genome searching. DragonFly port maintained by [email protected]. |
| biology/lamarc | DragonFly | 2.1.8_1,1 | biology/lamarc 2.1.8_1,1: Package of programs for computing population parameters. DragonFly port maintained by [email protected]. |
| biology/libbigwig | DragonFly | 0.4.8 | biology/libbigwig 0.4.8: C library for handling bigWig files (containing genomic data). DragonFly port maintained by [email protected]. |
| biology/libcombine | DragonFly | 0.2.20 | biology/libcombine 0.2.20: C++ library for working with the COMBINE archive format. DragonFly port maintained by [email protected]. |
| biology/libgff | DragonFly | 2.0.0 | biology/libgff 2.0.0: GFF/GTF parsing library based on GCLib. DragonFly port maintained by [email protected]. |
| biology/libgtextutils | DragonFly | 0.7 | biology/libgtextutils 0.7: Gordon's text utilities. DragonFly port maintained by [email protected]. |
| biology/libneurosim | DragonFly | 1.2.0_1 | biology/libneurosim 1.2.0_1: Common interfaces for neuronal simulators. DragonFly port maintained by [email protected]. |
| biology/libnuml | DragonFly | 1.1.7 | biology/libnuml 1.1.7: C++ library for Numerical Markup Language. DragonFly port maintained by [email protected]. |
| biology/libsbml | DragonFly | 5.20.4_1 | biology/libsbml 5.20.4_1: API Library for Working with SBML File. DragonFly port maintained by [email protected]. |
| biology/libsedml | DragonFly | 2.0.32 | biology/libsedml 2.0.32: C++ SED-ML library. DragonFly port maintained by [email protected]. |
| biology/mafft | DragonFly | 7.267_1 | biology/mafft 7.267_1: Multiple alignment program for amino acid or nucleotide sequences. DragonFly port maintained by [email protected]. |
| biology/mapm3 | DragonFly | 3.0_1 | biology/mapm3 3.0_1: Constructs linkage maps of markers segregating in experimental crosses. DragonFly port maintained by [email protected]. |
| biology/megahit | DragonFly | 1.2.9_1 | biology/megahit 1.2.9_1: Ultra-fast single-node large and complex metagenomics assembly. DragonFly port maintained by [email protected]. |
| biology/migrate | DragonFly | 5.0.6_2 | biology/migrate 5.0.6_2: Program to estimate population sizes and migration rates. DragonFly port maintained by [email protected]. |
| biology/minimap2 | DragonFly | 2.28_1 | biology/minimap2 2.28_1: Pairwise aligner for genomic and spliced nucleotide sequences. DragonFly port maintained by [email protected]. |
| biology/mmseqs2 | DragonFly | 17.b804.f | biology/mmseqs2 17.b804.f: Ultra fast and sensitive sequence search and clustering suite. DragonFly port maintained by [email protected]. |
| biology/mothur | DragonFly | 1.48.2 | biology/mothur 1.48.2: Software for bioinformatics of the microbial ecology community. DragonFly port maintained by [email protected]. |
| biology/mrbayes | DragonFly | 3.2.7_2 | biology/mrbayes 3.2.7_2: Bayesian inference of phylogeny. DragonFly port maintained by [email protected]. |
| biology/mummer | DragonFly | 4.0.1 | biology/mummer 4.0.1: Modular system for rapid whole genome alignment. DragonFly port maintained by [email protected]. |
| biology/muscle | DragonFly | 3.8.1551 | biology/muscle 3.8.1551: MUltiple Sequence Comparison by Log-Expectation. DragonFly port maintained by [email protected]. |
| biology/ncbi-entrez-direct | DragonFly | 14.9.20210423_25 | biology/ncbi-entrez-direct 14.9.20210423_25: Access to the NCBI's suite of interconnected databases. DragonFly port maintained by [email protected]. |
| biology/ncbi-toolkit | DragonFly | 2017.01.06_9 | biology/ncbi-toolkit 2017.01.06_9: NCBI development toolkit, including BLAST 2 and GenBank/Entrez support. DragonFly port maintained by [email protected]. |
| biology/ngs-sdk | DragonFly | 3.0.1 | biology/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-AcePerl | DragonFly | 1.92_5 | biology/p5-AcePerl 1.92_5: Perl5 interface to the ACEDB genome database system. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-ASN1-EntrezGene | DragonFly | 1.73_2,1 | biology/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-Cluster | DragonFly | 1.7.3_1 | biology/p5-Bio-Cluster 1.7.3_1: BioPerl cluster modules. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-Coordinate | DragonFly | 1.007001 | biology/p5-Bio-Coordinate 1.007001: Modules for working with biological coordinates. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-DB-EMBL | DragonFly | 1.7.4 | biology/p5-Bio-DB-EMBL 1.7.4: Database object interface for EMBL entry retrieval. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-DB-NCBIHelper | DragonFly | 1.7.8 | biology/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-Das | DragonFly | 1.17_4 | biology/p5-Bio-Das 1.17_4: Client-side library for Distributed Genome Annotation System. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-FeatureIO | DragonFly | 1.6.905 | biology/p5-Bio-FeatureIO 1.6.905: Handler for FeatureIO. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-GFF3 | DragonFly | 2.0_2 | biology/p5-Bio-GFF3 2.0_2: Fast low-level functions for parsing and formatting GFF3. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-Glite | DragonFly | 0.10_2 | biology/p5-Bio-Glite 0.10_2: Perl Interface to G-language. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-Graphics | DragonFly | 2.40_2 | biology/p5-Bio-Graphics 2.40_2: Generate GD Images of Bio::Seq Objects. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-MAGETAB | DragonFly | 1.31_2 | biology/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-NEXUS | DragonFly | 0.78_1 | biology/p5-Bio-NEXUS 0.78_1: Object-oriented Perl API for the NEXUS file format. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-Phylo | DragonFly | 2.0.1 | biology/p5-Bio-Phylo 2.0.1: Phylogenetic analysis using Perl. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-SCF | DragonFly | 1.03_2 | biology/p5-Bio-SCF 1.03_2: Read and Update SCF Chromatographic Sequence Files. DragonFly port maintained by [email protected]. |
| biology/p5-Bio-Variation | DragonFly | 1.7.5 | biology/p5-Bio-Variation 1.7.5: BioPerl variation-related functionality. DragonFly port maintained by [email protected]. |
| biology/p5-BioPerl | DragonFly | 1.007008 | biology/p5-BioPerl 1.007008: Collection of Perl modules for bioinformatics. DragonFly port maintained by [email protected]. |
| biology/p5-BioPerl-Run | DragonFly | 1.007003 | biology/p5-BioPerl-Run 1.007003: Wrapper modules for common bioinformatics tools. DragonFly port maintained by [email protected]. |
| biology/p5-TrimGalore | DragonFly | 0.6.10 | biology/p5-TrimGalore 0.6.10: Wrapper around Cutadapt and FastQC for adapter and quality trimming. DragonFly port maintained by [email protected]. |
| biology/p5-transdecoder | DragonFly | 5.7.1 | biology/p5-transdecoder 5.7.1: Identify candidate coding regions within transcript sequences. DragonFly port maintained by [email protected]. |
| biology/paml | DragonFly | 4.10.7 | biology/paml 4.10.7: Phylogenetic Analysis by Maximum Likelihood (PAML). DragonFly port maintained by [email protected]. |
| biology/pbbam | DragonFly | 0.18.0_11 | biology/pbbam 0.18.0_11: PacBio BAM C++ library, with SWIG bindings. DragonFly port maintained by [email protected]. |
| biology/peak-classifier | DragonFly | 0.1.4.13_1 | biology/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-merger | DragonFly | 0.9.6_1 | biology/pear-merger 0.9.6_1: Memory-efficient and highly accurate paired-end read merger. DragonFly port maintained by [email protected]. |
| biology/phyml | DragonFly | 3.3.20220408_1,1 | biology/phyml 3.3.20220408_1,1: Simple, fast, and accurate algorithm to estimate large phylogenies. DragonFly port maintained by [email protected]. |
| biology/picard-tools | DragonFly | 2.22.9 | biology/picard-tools 2.22.9: CLI tools for manipulating high-throughput sequencing (HTS) data. DragonFly port maintained by [email protected]. |
| biology/plink | DragonFly | 1.90.b6.17_5 | biology/plink 1.90.b6.17_5: Whole genome association analysis toolset. DragonFly port maintained by [email protected]. |
| biology/pooler | DragonFly | 1.89 | biology/pooler 1.89: Optimise DNA sequencing primer-set combinations. DragonFly port maintained by [email protected]. |
| biology/preseq | DragonFly | 3.2.0 | biology/preseq 3.2.0: Predict yield of distinct reads from a genomic library. DragonFly port maintained by [email protected]. |
| biology/primer3 | DragonFly | 2.3.6 | biology/primer3 2.3.6: Primer3 helps to choose primers for PCR reactions. DragonFly port maintained by [email protected]. |
| biology/prodigal | DragonFly | 2.6.3.16 | biology/prodigal 2.6.3.16: Protein-coding gene prediction for prokaryotic genomes. DragonFly port maintained by [email protected]. |
| biology/prodigy-lig | DragonFly | 1.1.3 | biology/prodigy-lig 1.1.3: Prediction of protein-small molecule binding affinities. DragonFly port maintained by [email protected]. |
| biology/protomol | DragonFly | 2.0.3_16 | biology/protomol 2.0.3_16: OO, component based, framework for molecular dynamics (MD) simulations. DragonFly port maintained by [email protected]. |
| biology/psi88 | DragonFly | 1.0_17 | biology/psi88 1.0_17: Plotting wavefunctions (molecular orbitals) in 3D. DragonFly port maintained by [email protected]. |
| biology/py-Genesis-PyAPI | DragonFly | 1.2.1_1 | biology/py-Genesis-PyAPI 1.2.1_1: API for the Genesis platform for genetics information processing. DragonFly port maintained by [email protected]. |
| biology/py-PySCeS | DragonFly | 1.2.2 | biology/py-PySCeS 1.2.2: Python Simulator for Cellular Systems. DragonFly port maintained by [email protected]. |
| biology/py-bcbio-gff | DragonFly | 0.7.1_1 | biology/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-format | DragonFly | 2.1.16_1 | biology/py-biom-format 2.1.16_1: Biological Observation Matrix (BIOM) Format Project. DragonFly port maintained by [email protected]. |
| biology/py-biopython | DragonFly | 1.85_1 | biology/py-biopython 1.85_1: Collection of Python modules for bioinformatics. DragonFly port maintained by [email protected]. |
| biology/py-biosig | DragonFly | 2.6.1_1 | biology/py-biosig 2.6.1_1: Library for reading and writing different biosignal data format. DragonFly port maintained by [email protected]. |
| biology/py-bx-python | DragonFly | 0.13.0_1 | biology/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-crossmap | DragonFly | 0.7.3_1 | biology/py-crossmap 0.7.3_1: Lift over genomics coordinates between assemblies. DragonFly port maintained by [email protected]. |
| biology/py-cutadapt | DragonFly | 5.0_1 | biology/py-cutadapt 5.0_1: Trim adapters from high-throughput sequencing reads. DragonFly port maintained by [email protected]. |
| biology/py-deeptools | DragonFly | 3.5.2_1 | biology/py-deeptools 3.5.2_1: User-friendly tools for exploring deep-sequencing data. DragonFly port maintained by [email protected]. |
| biology/py-deeptoolsintervals | DragonFly | 0.1.9_1 | biology/py-deeptoolsintervals 0.1.9_1: Python interface for deepTools interval trees. DragonFly port maintained by [email protected]. |
| biology/py-dna-features-viewer | DragonFly | 3.1.3_1 | biology/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-dnaio | DragonFly | 1.2.3 | biology/py-dnaio 1.2.3: Read and write FASTQ and FASTA. DragonFly port maintained by [email protected]. |
| biology/py-ete3 | DragonFly | 3.1.3_1 | biology/py-ete3 3.1.3_1: Framework for the analysis and visualization of trees. DragonFly port maintained by [email protected]. |
BSD Ports