BSD Ports

All ports

PortSystemVersionComment
biology/poolerFreeBSD1.89biology/pooler 1.89: Optimise DNA sequencing primer-set combinations. FreeBSD port maintained by [email protected].
biology/preseqFreeBSD3.2.0biology/preseq 3.2.0: Predict yield of distinct reads from a genomic library. FreeBSD port maintained by [email protected].
biology/primer3FreeBSD2.3.6biology/primer3 2.3.6: Primer3 helps to choose primers for PCR reactions. FreeBSD port maintained by [email protected].
biology/prodigalFreeBSD2.6.3.16biology/prodigal 2.6.3.16: Protein-coding gene prediction for prokaryotic genomes. FreeBSD port maintained by [email protected].
biology/prodigy-ligFreeBSD1.1.4biology/prodigy-lig 1.1.4: Prediction of protein-small molecule binding affinities. FreeBSD port maintained by [email protected].
biology/protomolFreeBSD2.0.3_16biology/protomol 2.0.3_16: OO, component based, framework for molecular dynamics (MD) simulations. FreeBSD port maintained by [email protected].
biology/psi88FreeBSD1.0_17biology/psi88 1.0_17: Plotting wavefunctions (molecular orbitals) in 3D. FreeBSD port maintained by [email protected].
biology/py-Genesis-PyAPIFreeBSD1.2.1_1biology/py-Genesis-PyAPI 1.2.1_1: API for the Genesis platform for genetics information processing. FreeBSD port maintained by [email protected].
biology/py-PySCeSFreeBSD1.2.3biology/py-PySCeS 1.2.3: Python Simulator for Cellular Systems. FreeBSD port maintained by [email protected].
biology/py-bcbio-gffFreeBSD0.7.1_1biology/py-bcbio-gff 0.7.1_1: Read and write Generic Feature Format (GFF) with Biopython integration. FreeBSD port maintained by [email protected].
biology/py-biom-formatFreeBSD2.1.16_3biology/py-biom-format 2.1.16_3: Biological Observation Matrix (BIOM) Format Project. FreeBSD port maintained by [email protected].
biology/py-biopythonFreeBSD1.85_4biology/py-biopython 1.85_4: Collection of Python modules for bioinformatics. FreeBSD port maintained by [email protected].
biology/py-biosigFreeBSD3.9.5_1biology/py-biosig 3.9.5_1: Library for reading and writing different biosignal data format. FreeBSD port maintained by [email protected].
biology/py-bx-pythonFreeBSD0.15.1biology/py-bx-python 0.15.1: Python module for reading, manipulating and writing genomic data sets. FreeBSD port maintained by [email protected].
biology/py-crossmapFreeBSD0.7.4biology/py-crossmap 0.7.4: Lift over genomics coordinates between assemblies. FreeBSD port maintained by [email protected].
biology/py-cutadaptFreeBSD5.2biology/py-cutadapt 5.2: Trim adapters from high-throughput sequencing reads. FreeBSD port maintained by [email protected].
biology/py-deeptoolsFreeBSD3.5.6biology/py-deeptools 3.5.6: User-friendly tools for exploring deep-sequencing data. FreeBSD port maintained by [email protected].
biology/py-deeptoolsintervalsFreeBSD0.1.9_1biology/py-deeptoolsintervals 0.1.9_1: Python interface for deepTools interval trees. FreeBSD port maintained by [email protected].
biology/py-dna-features-viewerFreeBSD3.1.5biology/py-dna-features-viewer 3.1.5: Python library to visualize DNA features, e.g. GenBank or Gff files. FreeBSD port maintained by [email protected].
biology/py-dnaioFreeBSD1.2.4biology/py-dnaio 1.2.4: Read and write FASTQ and FASTA. FreeBSD port maintained by [email protected].
biology/py-ete3FreeBSD3.1.3_5biology/py-ete3 3.1.3_5: Framework for the analysis and visualization of trees. FreeBSD port maintained by [email protected].
biology/py-gffutilsFreeBSD0.14biology/py-gffutils 0.14: Work with GFF and GTF files in a flexible database framework. FreeBSD port maintained by [email protected].
biology/py-goatoolsFreeBSD1.6.5biology/py-goatools 1.6.5: Tools for processing and visualizing Gene Ontology terms. FreeBSD port maintained by [email protected].
biology/py-gtfparseFreeBSD3.0.2biology/py-gtfparse 3.0.2: Parsing tools for GTF (gene transfer format) files. FreeBSD port maintained by [email protected].
biology/py-hitsFreeBSD0.5.1biology/py-hits 0.5.1: Utilities for processing high-throughput sequencing experiments. FreeBSD port maintained by [email protected].
biology/py-htseqFreeBSD2.1.2_2biology/py-htseq 2.1.2_2: Python library to facilitate programmatic analysis of sequence data. FreeBSD port maintained by [email protected].
biology/py-libnumlFreeBSD1.1.8biology/py-libnuml 1.1.8: Numerical Markup Language for Python. FreeBSD port maintained by [email protected].
biology/py-libsedmlFreeBSD2.0.34biology/py-libsedml 2.0.34: SED-ML library for Python. FreeBSD port maintained by [email protected].
biology/py-loompyFreeBSD3.0.8biology/py-loompy 3.0.8: Work with .loom files for single-cell RNA-seq data. FreeBSD port maintained by [email protected].
biology/py-macs3FreeBSD3.0.5biology/py-macs3 3.0.5: Peak caller aimed at transcription factor binding sites. FreeBSD port maintained by [email protected].
biology/py-mrcfileFreeBSD1.5.4biology/py-mrcfile 1.5.4: MRC file I/O library which is used in structural biology. FreeBSD port maintained by [email protected].
biology/py-multiqcFreeBSD1.35biology/py-multiqc 1.35: Aggregate bioinformatics analysis reports across samples and tools. FreeBSD port maintained by [email protected].
biology/py-newickFreeBSD1.11.0biology/py-newick 1.11.0: Python module to read and write the Newick format. FreeBSD port maintained by [email protected].
biology/py-ont-fast5-apiFreeBSD4.1.3biology/py-ont-fast5-api 4.1.3: Interface to HDF5 files in Oxford Nanopore .fast5 format. FreeBSD port maintained by [email protected].
biology/py-pandas-charmFreeBSD0.3.0_3biology/py-pandas-charm 0.3.0_3: Library for getting character matrices into and out of pandas. FreeBSD port maintained by [email protected].
biology/py-py2bitFreeBSD1.0.1biology/py-py2bit 1.0.1: Python interface for 2bit packed nucleotide files. FreeBSD port maintained by [email protected].
biology/py-pybigwigFreeBSD0.3.22_1biology/py-pybigwig 0.3.22_1: Python access to bigWig files using libBigWig. FreeBSD port maintained by [email protected].
biology/py-pydeseq2FreeBSD0.5.4biology/py-pydeseq2 0.5.4: Python implementation of the popular DESeq2 R package. FreeBSD port maintained by [email protected].
biology/py-pyfaidxFreeBSD0.9.1biology/py-pyfaidx 0.9.1: Efficient pythonic random access to fasta subsequences. FreeBSD port maintained by [email protected].
biology/py-pyrodigalFreeBSD3.7.1biology/py-pyrodigal 3.7.1: Python binding for Prodigal, an ORF finder for genomes and metagenomes. FreeBSD port maintained by [email protected].
biology/py-pysamFreeBSD0.24.1biology/py-pysam 0.24.1: Python module for reading, manipulating and writing genomic data sets. FreeBSD port maintained by [email protected].
biology/py-python-libsbmlFreeBSD5.21.2_1biology/py-python-libsbml 5.21.2_1: LibSBML Python API. FreeBSD port maintained by [email protected].
biology/py-pywgsimFreeBSD0.6.0biology/py-pywgsim 0.6.0: Modified wgsim genomic data simulator. FreeBSD port maintained by [email protected].
biology/py-resdkFreeBSD22.2.3biology/py-resdk 22.2.3: Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics. FreeBSD port maintained by [email protected].
biology/py-scikit-bioFreeBSD0.7.4biology/py-scikit-bio 0.7.4: Data structures, algorithms, educational resources for bioinformatics. FreeBSD port maintained by [email protected].
biology/py-valeriusFreeBSD0.2_1biology/py-valerius 0.2_1: Python bioinformatics tools. FreeBSD port maintained by [email protected].
biology/py-xenaPythonFreeBSD1.0.14_1biology/py-xenaPython 1.0.14_1: API for Xena Hub to access genetic information shared through the hub. FreeBSD port maintained by [email protected].
biology/pyfastaFreeBSD0.5.2_7biology/pyfasta 0.5.2_7: Fast, memory-efficient, pythonic access to fasta sequence files. FreeBSD port maintained by [email protected].
biology/python-nexusFreeBSD2.9.0_1biology/python-nexus 2.9.0_1: Generic nexus file format reader for python. FreeBSD port maintained by [email protected].
biology/rainbowFreeBSD2.0.4biology/rainbow 2.0.4: Efficient clustering and assembling of short reads, especially for RAD. FreeBSD port maintained by [email protected].
biology/ramplerFreeBSD2.1.1biology/rampler 2.1.1: Standalone module for sampling genomic sequences. FreeBSD port maintained by [email protected].
biology/readseqFreeBSD2.1.19_2biology/readseq 2.1.19_2: Read and reformat biosequences, Java command-line version. FreeBSD port maintained by [email protected].
biology/rna-seqFreeBSD0.2.0biology/rna-seq 0.2.0: Metaport for RNA-Seq analysis. FreeBSD port maintained by [email protected].
biology/ruby-bioFreeBSD1.5.1biology/ruby-bio 1.5.1: Integrated environment for Bioinformatics written in Ruby. FreeBSD port maintained by [email protected].
biology/rubygem-bioFreeBSD2.0.6biology/rubygem-bio 2.0.6: Integrated environment for Bioinformatics written in Ruby. FreeBSD port maintained by [email protected].
biology/rubygem-bio-executablesFreeBSD1.0.0biology/rubygem-bio-executables 1.0.0: Collection of miscellaneous utilities for bioinformatics. FreeBSD port maintained by [email protected].
biology/rubygem-bio-old-biofetch-emulatorFreeBSD1.0.0biology/rubygem-bio-old-biofetch-emulator 1.0.0: Emulate Bio::Fetch object. FreeBSD port maintained by [email protected].
biology/rubygem-bio-shellFreeBSD1.0.1biology/rubygem-bio-shell 1.0.1: Command-line interface on BioRuby. FreeBSD port maintained by [email protected].
biology/salmonFreeBSD1.10.3_2biology/salmon 1.10.3_2: Transcript-level quantification of RNA-seq from lightweight alignments. FreeBSD port maintained by [email protected].
biology/sam2pairwiseFreeBSD1.0.0biology/sam2pairwise 1.0.0: Show pairwise alignment for each read in a SAM file. FreeBSD port maintained by [email protected].
biology/samtoolsFreeBSD1.24biology/samtools 1.24: Tools for manipulating next-generation sequencing data. FreeBSD port maintained by [email protected].
biology/scrmFreeBSD1.7.4_1biology/scrm 1.7.4_1: Coalescent simulator for biological sequences. FreeBSD port maintained by [email protected].
biology/seaviewFreeBSD5.1,1biology/seaview 5.1,1: Multiple DNA/protein sequence alignment editor. FreeBSD port maintained by [email protected].
biology/seqanFreeBSD2.4.0biology/seqan 2.4.0: C++ sequence analysis template library. FreeBSD port maintained by h2+[email protected].
biology/seqan-appsFreeBSD2.4.0_11biology/seqan-apps 2.4.0_11: Official bioinformatic applications based on the SeqAn library. FreeBSD port maintained by h2+[email protected].
biology/seqan1FreeBSD1.3.1_4biology/seqan1 1.3.1_4: C++ Sequence Analysis Library. FreeBSD port maintained by h2+[email protected].
biology/seqan3FreeBSD3.4.2biology/seqan3 3.4.2: C++ header-only library for biological sequence analysis. FreeBSD port maintained by [email protected].
biology/seqkitFreeBSD2.14.0_1biology/seqkit 2.14.0_1: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation. FreeBSD port maintained by [email protected].
biology/seqtkFreeBSD1.5biology/seqtk 1.5: Tool for processing sequences in FASTA/FASTQ format. FreeBSD port maintained by [email protected].
biology/seqwishFreeBSD0.7.12_1biology/seqwish 0.7.12_1: Alignment to variation graph inducer. FreeBSD port maintained by [email protected].
biology/sigviewerFreeBSD0.6.4.13_3biology/sigviewer 0.6.4.13_3: Viewing application for biosignals. FreeBSD port maintained by [email protected].
biology/slclustFreeBSD2010.02.02biology/slclust 2010.02.02: Single-linkage clustering with Jaccard similarity. FreeBSD port maintained by [email protected].
biology/smithwatermanFreeBSDg20160702biology/smithwaterman g20160702: Smith-waterman-gotoh alignment algorithm. FreeBSD port maintained by [email protected].
biology/spoaFreeBSD4.1.5biology/spoa 4.1.5: C++ implementation of the partial order alignment (POA) algorithm. FreeBSD port maintained by [email protected].
biology/sra-toolsFreeBSD3.4.1_3biology/sra-tools 3.4.1_3: NCBI's toolkit for handling data in INSDC Sequence Read Archives. FreeBSD port maintained by [email protected].
biology/stacksFreeBSD2.68biology/stacks 2.68: Software pipeline for building loci from short-read sequences. FreeBSD port maintained by [email protected].
biology/starFreeBSD2.7.11.a_1biology/star 2.7.11.a_1: Spliced Transcripts Alignment to a Reference. FreeBSD port maintained by [email protected].
biology/stringtieFreeBSD2.1.1biology/stringtie 2.1.1: Transcript assembly and quantification for RNA-seq. FreeBSD port maintained by [email protected].
biology/subreadFreeBSD2.1.1biology/subread 2.1.1: High-performance read alignment, quantification and mutation discovery. FreeBSD port maintained by [email protected].
biology/tRNAscan-SEFreeBSD2.0.11biology/tRNAscan-SE 2.0.11: Searching for tRNA genes in genomic sequence. FreeBSD port maintained by [email protected].
biology/tabixppFreeBSD1.1.2biology/tabixpp 1.1.2: C++ wrapper to tabix indexer. FreeBSD port maintained by [email protected].
biology/taxonkitFreeBSD0.20.0_8biology/taxonkit 0.20.0_8: Practical and efficient NCBI taxonomy toolkit. FreeBSD port maintained by [email protected].
biology/treekinFreeBSD0.5.1_7biology/treekin 0.5.1_7: Efficient computation of RNA folding dynamics. FreeBSD port maintained by [email protected].
biology/treepuzzleFreeBSD5.2biology/treepuzzle 5.2: Maximum likelihood phylogeny reconstruction using quartets. FreeBSD port maintained by [email protected].
biology/trimadapFreeBSD0.1.4biology/trimadap 0.1.4: Trim adapter sequences from Illumina data using heuristic rules. FreeBSD port maintained by [email protected].
biology/trimmomaticFreeBSD0.39_2biology/trimmomatic 0.39_2: Flexible read trimming tool for Illumina NGS data. FreeBSD port maintained by [email protected].
biology/ucsc-userappsFreeBSD502biology/ucsc-userapps 502: Command line tools from the UCSC Genome Browser project. FreeBSD port maintained by [email protected].
biology/ugeneFreeBSD53.1_1biology/ugene 53.1_1: Integrated bioinformatics toolkit. FreeBSD port maintained by [email protected].
biology/unikmerFreeBSD0.20.0_27biology/unikmer 0.20.0_27: Toolkit for nucleic acid k-mer analysis, set operations on k-mers. FreeBSD port maintained by [email protected].
biology/vcf-splitFreeBSD0.1.5.10_1biology/vcf-split 0.1.5.10_1: Split a multi-sample VCF into single-sample VCFs. FreeBSD port maintained by [email protected].
biology/vcf2hapFreeBSD0.1.6.7_1biology/vcf2hap 0.1.6.7_1: Generate .hap file from VCF for haplohseq. FreeBSD port maintained by [email protected].
biology/vcflibFreeBSD1.0.15biology/vcflib 1.0.15: C++ library and CLI tools for parsing and manipulating VCF files. FreeBSD port maintained by [email protected].
biology/vcftoolsFreeBSD0.1.17biology/vcftools 0.1.17: Tools for working with VCF genomics files. FreeBSD port maintained by [email protected].
biology/velvetFreeBSD1.2.10_2biology/velvet 1.2.10_2: Sequence assembler for very short reads. FreeBSD port maintained by [email protected].
biology/viennarnaFreeBSD2.7.2biology/viennarna 2.7.2: Alignment tools for the structural analysis of RNA. FreeBSD port maintained by [email protected].
biology/vsearchFreeBSD2.32.0biology/vsearch 2.32.0: Versatile open-source tool for metagenomics. FreeBSD port maintained by [email protected].
biology/vtFreeBSD0.57721_3biology/vt 0.57721_3: Discovers short variants from Next Generation Sequencing data. FreeBSD port maintained by [email protected].
biology/wfa2-libFreeBSD2.3.6biology/wfa2-lib 2.3.6: Exact gap-affine algorithm using homology to accelerate alignment. FreeBSD port maintained by [email protected].
biology/wiseFreeBSD2.4.1_1biology/wise 2.4.1_1: Intelligent algorithms for DNA searches. FreeBSD port maintained by [email protected].
cad/Clipper2FreeBSD2.0.1cad/Clipper2 2.0.1: A Polygon Clipping and Offsetting library (in C++, C# & Delphi). FreeBSD port maintained by [email protected].