| biology/fastdnaml | FreeBSD | 1.2.2_2 | biology/fastdnaml 1.2.2_2: Faster DNAML, makes phylogenetic trees using maximum likelihood. FreeBSD port maintained by [email protected]. |
| biology/fastool | FreeBSD | 0.1.4 | biology/fastool 0.1.4: Simple and quick FastQ and FastA tool for file reading and conversion. FreeBSD port maintained by [email protected]. |
| biology/fastp | FreeBSD | 1.4.0 | biology/fastp 1.4.0: Ultra-fast all-in-one FASTQ preprocessor. FreeBSD port maintained by [email protected]. |
| biology/fastq-trim | FreeBSD | 0.1.4 | biology/fastq-trim 0.1.4: Lightening fast sequence read trimmer. FreeBSD port maintained by [email protected]. |
| biology/fastqc | FreeBSD | 0.12.1_2 | biology/fastqc 0.12.1_2: Quality control tool for high throughput sequence data. FreeBSD port maintained by [email protected]. |
| biology/fasttree | FreeBSD | 2.1.11 | biology/fasttree 2.1.11: Approximately-maximum-likelihood phylogenetic trees from alignments. FreeBSD port maintained by [email protected]. |
| biology/fastx-toolkit | FreeBSD | 0.0.14_1 | biology/fastx-toolkit 0.0.14_1: CLI tools for Short-Reads FASTA/FASTQ files preprocessing. FreeBSD port maintained by [email protected]. |
| biology/fermi-lite | FreeBSD | 0.1.13_2 | biology/fermi-lite 0.1.13_2: Library and tool for assembling Illumina short reads in small regions. FreeBSD port maintained by [email protected]. |
| biology/figtree | FreeBSD | 1.4.5.p.6 | biology/figtree 1.4.5.p.6: Graphical viewer of phylogenetic trees. FreeBSD port maintained by [email protected]. |
| biology/flash | FreeBSD | 1.2.11 | biology/flash 1.2.11: Fast Length Adjustment of SHort reads. FreeBSD port maintained by [email protected]. |
| biology/fluctuate | FreeBSD | 1.40 | biology/fluctuate 1.40: Program to fit population models. FreeBSD port maintained by [email protected]. |
| biology/freebayes | FreeBSD | 1.3.10 | biology/freebayes 1.3.10: Bayesian haplotype-based polymorphism discovery and genotyping. FreeBSD port maintained by [email protected]. |
| biology/garlic | FreeBSD | 1.6_1 | biology/garlic 1.6_1: Molecular viewer, editor, and visualization program. FreeBSD port maintained by [email protected]. |
| biology/gatk | FreeBSD | 4.7.0.0 | biology/gatk 4.7.0.0: Genome Analysis Toolkit. FreeBSD port maintained by [email protected]. |
| biology/gcta | FreeBSD | 1.94.1_6 | biology/gcta 1.94.1_6: Genome-wide Complex Trait Analysis. FreeBSD port maintained by [email protected]. |
| biology/gemma | FreeBSD | 0.98.5_3 | biology/gemma 0.98.5_3: Genome-wide Efficient Mixed Model Association. FreeBSD port maintained by [email protected]. |
| biology/generand | FreeBSD | 0.1.2_1 | biology/generand 0.1.2_1: Generate random genomic data in FASTA/FASTQ, SAM, or VCF format. FreeBSD port maintained by [email protected]. |
| biology/gff2ps | FreeBSD | 0.98l | biology/gff2ps 0.98l: Convert gff-formatted genomic data sets to PostScript. FreeBSD port maintained by [email protected]. |
| biology/gffread | FreeBSD | 0.12.9 | biology/gffread 0.12.9: GFF/GTF format conversions, filtering, FASTA extraction, etc. FreeBSD port maintained by [email protected]. |
| biology/gkl | FreeBSD | 0.9.1_3 | biology/gkl 0.9.1_3: Accelerated kernel library for genomics. FreeBSD port maintained by [email protected]. |
| biology/gmap | FreeBSD | 2025.07.31_1 | biology/gmap 2025.07.31_1: Genomic Mapping and Alignment Program for mRNA and EST Sequences. FreeBSD port maintained by [email protected]. |
| biology/graphlan | FreeBSD | 1.1.3_1 | biology/graphlan 1.1.3_1: High-quality circular representations of taxonomic, phylogenetic trees. FreeBSD port maintained by [email protected]. |
| biology/groopm | FreeBSD | 0.3.4_8 | biology/groopm 0.3.4_8: Metagenomic binning suite. FreeBSD port maintained by [email protected]. |
| biology/haplohseq | FreeBSD | 0.1.2.3_4 | biology/haplohseq 0.1.2.3_4: Identify regions of allelic imbalance. FreeBSD port maintained by [email protected]. |
| biology/hhsuite | FreeBSD | 3.3.0_3 | biology/hhsuite 3.3.0_3: Remote protein homology detection suite. FreeBSD port maintained by [email protected]. |
| biology/hisat2 | FreeBSD | 2.2.3 | biology/hisat2 2.2.3: Alignment program for mapping next-generation sequencing reads. FreeBSD port maintained by [email protected]. |
| biology/hmmer | FreeBSD | 3.4 | biology/hmmer 3.4: Profile hidden Markov models for biological sequence analysis. FreeBSD port maintained by [email protected]. |
| biology/htslib | FreeBSD | 1.24_1 | biology/htslib 1.24_1: C library for high-throughput sequencing data formats. FreeBSD port maintained by [email protected]. |
| biology/hyphy | FreeBSD | 2.5.103 | biology/hyphy 2.5.103: Hypothesis testing using Phylogenies. FreeBSD port maintained by [email protected]. |
| biology/igv | FreeBSD | 2.19.8 | biology/igv 2.19.8: Visualization tool for genomic datasets. FreeBSD port maintained by [email protected]. |
| biology/infernal | FreeBSD | 1.1.5 | biology/infernal 1.1.5: Search sequence databases for structural RNA homologs. FreeBSD port maintained by [email protected]. |
| biology/iolib | FreeBSD | 1.16.0 | biology/iolib 1.16.0: General purpose trace file (and Experiment File) reading interface. FreeBSD port maintained by [email protected]. |
| biology/iqtree | FreeBSD | 3.1.4 | biology/iqtree 3.1.4: Efficient phylogenomic software by maximum likelihood. FreeBSD port maintained by [email protected]. |
| biology/jalview | FreeBSD | 2.11.5.1 | biology/jalview 2.11.5.1: Viewer and editor for multiple sequence alignments. FreeBSD port maintained by [email protected]. |
| biology/jellyfish | FreeBSD | 2.3.1 | biology/jellyfish 2.3.1: Fast, memory-efficient counting of k-mers in DNA. FreeBSD port maintained by [email protected]. |
| biology/kallisto | FreeBSD | 0.52.0,1 | biology/kallisto 0.52.0,1: Quantify abundances of transcripts from RNA-Seq data. FreeBSD port maintained by [email protected]. |
| biology/kmcp | FreeBSD | 0.9.4_32 | biology/kmcp 0.9.4_32: Accurate metagenomic profiling & fast large-scale genome searching. FreeBSD port maintained by [email protected]. |
| biology/lamarc | FreeBSD | 2.1.8_2,1 | biology/lamarc 2.1.8_2,1: Package of programs for computing population parameters. FreeBSD port maintained by [email protected]. |
| biology/libbigwig | FreeBSD | 0.4.8 | biology/libbigwig 0.4.8: C library for handling bigWig files (containing genomic data). FreeBSD port maintained by [email protected]. |
| biology/libcombine | FreeBSD | 0.2.20_1 | biology/libcombine 0.2.20_1: C++ library for working with the COMBINE archive format. FreeBSD port maintained by [email protected]. |
| biology/libgff | FreeBSD | 2.0.1 | biology/libgff 2.0.1: GFF/GTF parsing library based on GCLib. FreeBSD port maintained by [email protected]. |
| biology/libgtextutils | FreeBSD | 0.7 | biology/libgtextutils 0.7: Gordon's text utilities. FreeBSD port maintained by [email protected]. |
| biology/libneurosim | FreeBSD | 1.2.0_1 | biology/libneurosim 1.2.0_1: Common interfaces for neuronal simulators. FreeBSD port maintained by [email protected]. |
| biology/libnuml | FreeBSD | 1.1.8 | biology/libnuml 1.1.8: C++ library for Numerical Markup Language. FreeBSD port maintained by [email protected]. |
| biology/libsbml | FreeBSD | 5.21.2 | biology/libsbml 5.21.2: API Library for Working with SBML File. FreeBSD port maintained by [email protected]. |
| biology/libsedml | FreeBSD | 2.0.34 | biology/libsedml 2.0.34: C++ SED-ML library. FreeBSD port maintained by [email protected]. |
| biology/linux-foldingathome | FreeBSD | 8.4.9_2 | biology/linux-foldingathome 8.4.9_2: Folding@home Client. FreeBSD port maintained by [email protected]. |
| biology/locarna | FreeBSD | 2.0.1 | biology/locarna 2.0.1: LocARNA provides several tools for the structural analysis of RNA. FreeBSD port maintained by [email protected]. |
| biology/mafft | FreeBSD | 7.267_1 | biology/mafft 7.267_1: Multiple alignment program for amino acid or nucleotide sequences. FreeBSD port maintained by [email protected]. |
| biology/mapm3 | FreeBSD | 3.0_1 | biology/mapm3 3.0_1: Constructs linkage maps of markers segregating in experimental crosses. FreeBSD port maintained by [email protected]. |
| biology/mashmap | FreeBSD | 3.1.3_1 | biology/mashmap 3.1.3_1: Fast approximate aligner for long DNA sequences. FreeBSD port maintained by [email protected]. |
| biology/mca-calling | FreeBSD | 0.1.0 | biology/mca-calling 0.1.0: Core tools for Mosaic Chromosomal Alteration event calling. FreeBSD port maintained by [email protected]. |
| biology/megahit | FreeBSD | 1.2.9.22 | biology/megahit 1.2.9.22: Ultra-fast single-node large and complex metagenomics assembly. FreeBSD port maintained by [email protected]. |
| biology/metaeuk | FreeBSD | 7 | biology/metaeuk 7: Gene discovery and annotation for large-scale eukaryotic metagenomics. FreeBSD port maintained by [email protected]. |
| biology/migrate | FreeBSD | 5.0.6_2 | biology/migrate 5.0.6_2: Program to estimate population sizes and migration rates. FreeBSD port maintained by [email protected]. |
| biology/minimap2 | FreeBSD | 2.31 | biology/minimap2 2.31: Pairwise aligner for genomic and spliced nucleotide sequences. FreeBSD port maintained by [email protected]. |
| biology/mmseqs2 | FreeBSD | 17.b804.f | biology/mmseqs2 17.b804.f: Ultra fast and sensitive sequence search and clustering suite. FreeBSD port maintained by [email protected]. |
| biology/molden | FreeBSD | 7.3,1 | biology/molden 7.3,1: Display molecular orbitals and electron densities in 2D and 3D. FreeBSD port maintained by [email protected]. |
| biology/mothur | FreeBSD | 1.48.6 | biology/mothur 1.48.6: Software for bioinformatics of the microbial ecology community. FreeBSD port maintained by [email protected]. |
| biology/mrbayes | FreeBSD | 3.2.7_2 | biology/mrbayes 3.2.7_2: Bayesian inference of phylogeny. FreeBSD port maintained by [email protected]. |
| biology/mummer | FreeBSD | 4.0.1 | biology/mummer 4.0.1: Modular system for rapid whole genome alignment. FreeBSD port maintained by [email protected]. |
| biology/muscle | FreeBSD | 5.1_1 | biology/muscle 5.1_1: MUltiple Sequence Comparison by Log-Expectation. FreeBSD port maintained by [email protected]. |
| biology/ncbi-blast+ | FreeBSD | 2.17.0_2 | biology/ncbi-blast+ 2.17.0_2: NCBI implementation of Basic Local Alignment Search Tool. FreeBSD port maintained by [email protected]. |
| biology/ncbi-cxx-toolkit | FreeBSD | 30.8.0_1 | biology/ncbi-cxx-toolkit 30.8.0_1: NCBI C++ Toolkit. FreeBSD port maintained by [email protected]. |
| biology/ncbi-entrez-direct | FreeBSD | 14.9.20210423_48 | biology/ncbi-entrez-direct 14.9.20210423_48: Access to the NCBI's suite of interconnected databases. FreeBSD port maintained by [email protected]. |
| biology/ncbi-toolkit | FreeBSD | 2017.01.06_10 | biology/ncbi-toolkit 2017.01.06_10: NCBI development toolkit, including BLAST 2 and GenBank/Entrez support. FreeBSD port maintained by [email protected]. |
| biology/ngs-sdk | FreeBSD | 3.0.1 | biology/ngs-sdk 3.0.1: Tools and libraries for using data in the INSDC Sequence Read Archives. FreeBSD port maintained by [email protected]. |
| biology/p5-AcePerl | FreeBSD | 1.92_5 | biology/p5-AcePerl 1.92_5: Perl5 interface to the ACEDB genome database system. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-ASN1-EntrezGene | FreeBSD | 1.73_2,1 | biology/p5-Bio-ASN1-EntrezGene 1.73_2,1: Regular expression-based Perl Parser for NCBI Entrez Gene. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Cluster | FreeBSD | 1.7.3_1 | biology/p5-Bio-Cluster 1.7.3_1: BioPerl cluster modules. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Coordinate | FreeBSD | 1.007001 | biology/p5-Bio-Coordinate 1.007001: Modules for working with biological coordinates. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-DB-EMBL | FreeBSD | 1.7.4 | biology/p5-Bio-DB-EMBL 1.7.4: Database object interface for EMBL entry retrieval. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-DB-NCBIHelper | FreeBSD | 1.7.8 | biology/p5-Bio-DB-NCBIHelper 1.7.8: Collection of routines useful for queries to NCBI databases. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Das | FreeBSD | 1.17_4 | biology/p5-Bio-Das 1.17_4: Client-side library for Distributed Genome Annotation System. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Das-Lite | FreeBSD | 2.11_1 | biology/p5-Bio-Das-Lite 2.11_1: Perl extension for the DAS (HTTP+XML) Protocol. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-FeatureIO | FreeBSD | 1.6.905 | biology/p5-Bio-FeatureIO 1.6.905: Handler for FeatureIO. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-GFF3 | FreeBSD | 2.0_2 | biology/p5-Bio-GFF3 2.0_2: Fast low-level functions for parsing and formatting GFF3. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Glite | FreeBSD | 0.10_2 | biology/p5-Bio-Glite 0.10_2: Perl Interface to G-language. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Graphics | FreeBSD | 2.40_2 | biology/p5-Bio-Graphics 2.40_2: Generate GD Images of Bio::Seq Objects. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-MAGETAB | FreeBSD | 1.31_2 | biology/p5-Bio-MAGETAB 1.31_2: Data model and utility API for the MAGE-TAB format. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-NEXUS | FreeBSD | 0.78_1 | biology/p5-Bio-NEXUS 0.78_1: Object-oriented Perl API for the NEXUS file format. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Phylo | FreeBSD | 2.0.1 | biology/p5-Bio-Phylo 2.0.1: Phylogenetic analysis using Perl. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-SCF | FreeBSD | 1.03_4 | biology/p5-Bio-SCF 1.03_4: Read and Update SCF Chromatographic Sequence Files. FreeBSD port maintained by [email protected]. |
| biology/p5-Bio-Variation | FreeBSD | 1.7.5 | biology/p5-Bio-Variation 1.7.5: BioPerl variation-related functionality. FreeBSD port maintained by [email protected]. |
| biology/p5-BioPerl | FreeBSD | 1.007008 | biology/p5-BioPerl 1.007008: Collection of Perl modules for bioinformatics. FreeBSD port maintained by [email protected]. |
| biology/p5-BioPerl-Run | FreeBSD | 1.007003 | biology/p5-BioPerl-Run 1.007003: Wrapper modules for common bioinformatics tools. FreeBSD port maintained by [email protected]. |
| biology/p5-transdecoder | FreeBSD | 6.0.0 | biology/p5-transdecoder 6.0.0: Identify candidate coding regions within transcript sequences. FreeBSD port maintained by [email protected]. |
| biology/paml | FreeBSD | 4.10.10 | biology/paml 4.10.10: Phylogenetic Analysis by Maximum Likelihood (PAML). FreeBSD port maintained by [email protected]. |
| biology/pbbam | FreeBSD | 0.18.0_14 | biology/pbbam 0.18.0_14: PacBio BAM C++ library, with SWIG bindings. FreeBSD port maintained by [email protected]. |
| biology/peak-classifier | FreeBSD | 0.1.4.13_2 | biology/peak-classifier 0.1.4.13_2: Classify ChIP/ATAC-Seq peaks based on features provided in a GFF. FreeBSD port maintained by [email protected]. |
| biology/pear-merger | FreeBSD | 0.9.6_1 | biology/pear-merger 0.9.6_1: Memory-efficient and highly accurate paired-end read merger. FreeBSD port maintained by [email protected]. |
| biology/phrap | FreeBSD | 1.090518 | biology/phrap 1.090518: Program for assembling shotgun DNA sequence data. FreeBSD port maintained by [email protected]. |
| biology/phred | FreeBSD | 0.020425.c | biology/phred 0.020425.c: Base calling and quality value assignment on DNA sequencing. FreeBSD port maintained by [email protected]. |
| biology/phyml | FreeBSD | 3.3.20220408_1,1 | biology/phyml 3.3.20220408_1,1: Simple, fast, and accurate algorithm to estimate large phylogenies. FreeBSD port maintained by [email protected]. |
| biology/picard-tools | FreeBSD | 3.5.0 | biology/picard-tools 3.5.0: CLI tools for manipulating high-throughput sequencing (HTS) data. FreeBSD port maintained by [email protected]. |
| biology/plink | FreeBSD | 1.90.b6.17_6 | biology/plink 1.90.b6.17_6: Whole genome association analysis toolset. FreeBSD port maintained by [email protected]. |
| biology/pooler | FreeBSD | 1.89 | biology/pooler 1.89: Optimise DNA sequencing primer-set combinations. FreeBSD port maintained by [email protected]. |
| biology/preseq | FreeBSD | 3.2.0 | biology/preseq 3.2.0: Predict yield of distinct reads from a genomic library. FreeBSD port maintained by [email protected]. |
| biology/primer3 | FreeBSD | 2.3.6 | biology/primer3 2.3.6: Primer3 helps to choose primers for PCR reactions. FreeBSD port maintained by [email protected]. |
| biology/prodigal | FreeBSD | 2.6.3.16 | biology/prodigal 2.6.3.16: Protein-coding gene prediction for prokaryotic genomes. FreeBSD port maintained by [email protected]. |
BSD Ports