biology
Bioinformatics and biology research tools
250 packages
Browse the complete collection of 250 FreeBSD biology packages available in the ports tree. Every package can be installed with a single pkg install command. The most popular packages in this category include htslib, p5-BioPerl, samtools.
Most Popular
htslib1.22C library for high-throughput sequencing data formats17 rdepsp5-BioPerl1.007008Collection of Perl modules for bioinformatics11 rdepssamtools1.22Tools for manipulating next-generation sequencing data10 rdepsbiolibc0.2.7Low-level high-performance bioinformatics library7 rdepsbcftools1.22Tools for manipulating next-generation sequencing data5 rdeps
All Packages
250 results
htslib1.22
C library for high-throughput sequencing data formats17 rdepsp5-BioPerl1.007008
Collection of Perl modules for bioinformatics11 rdepssamtools1.22
Tools for manipulating next-generation sequencing data10 rdepsbiolibc0.2.7
Low-level high-performance bioinformatics library7 rdepsbcftools1.22
Tools for manipulating next-generation sequencing data5 rdepsbedtools2.31.1
Toolset for genome set arithmetic such as intersect, union5 rdepsfastqc0.12.1
Quality control tool for high throughput sequence data5 rdepssra-tools3.3.0_2
NCBI's toolkit for handling data in INSDC Sequence Read Archives5 rdepsbwa0.7.19
Burrows-Wheeler sequence aligner4 rdepslibsbml5.20.5_1
API Library for Working with SBML File4 rdepspy311-biopython1.85_2
Collection of Python modules for bioinformatics4 rdepspy311-multiqc1.25.2_3
Aggregate bioinformatics analysis reports across samples and tools4 rdepspy311-pysam0.23.0_1
Python module for reading, manipulating and writing genomic data sets4 rdepsbamtools2.5.3
API and toolkit for handling BAM files3 rdepsbiolibc-tools0.1.5
High-performance bioinformatics tools based on biolibc3 rdepsbiosig2.6.1_2
Library for reading and writing different biosignal data format3 rdepsbowtie22.5.4
Ultrafast, memory-efficient short read aligner3 rdepscd-hit4.8.1_3
Clustering and comparing protein or nucleotide sequences3 rdepsfasda0.2.0.1
Fast and simple differential analysis3 rdepsfastq-trim0.1.4
Lightening fast sequence read trimmer3 rdepslibnuml1.1.7_1
C++ library for Numerical Markup Language3 rdepsrubygem-bio2.0.6
Integrated environment for Bioinformatics written in Ruby3 rdepsfreebayes1.3.9
Bayesian haplotype-based polymorphism discovery and genotyping2 rdepsgffread0.12.7
GFF/GTF format conversions, filtering, FASTA extraction, etc2 rdepshisat22.2.1_2
Alignment program for mapping next-generation sequencing reads2 rdepskallisto0.51.1_1,1
Quantify abundances of transcripts from RNA-Seq data2 rdepsp5-Bio-Cluster1.7.3_1
BioPerl cluster modules2 rdepspeak-classifier0.1.4.13_2
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF2 rdepspy311-cutadapt5.2
Trim adapters from high-throughput sequencing reads2 rdepspy311-macs22.2.9.1_1
Identify transcription factor binding sites2 rdepspy311-pyBigWig0.3.22_1
Python access to bigWig files using libBigWig2 rdepsseqtk1.5
Tool for processing sequences in FASTA/FASTQ format2 rdepstrimmomatic0.39
Flexible read trimming tool for Illumina NGS data2 rdepsJellyfish2.3.0_4
Fast, memory-efficient counting of k-mers in DNA1 rdepsR-cran-Biobase2.66.0
Base functions for Bioconductor1 rdepsR-cran-BiocGenerics0.52.0
S4 generic functions used in Bioconductor1 rdepsR-cran-BiocManager1.30.27
Convenient tool to install and update Bioconductor packages1 rdepsad2vcf0.1.6.19
Add allelic depth info from a SAM stream to a VCF file1 rdepsbamutil1.0.15
Utilities for working with SAM/BAM files1 rdepsbbmap39.34
BBMap short read aligner, and other bioinformatic tools1 rdepsbfcg20150417
Correct sequencing errors from Illumina sequencing data1 rdepsbio-mocha1.20_1
Bcftools plugin for mosaic chromosomal alteration analysis1 rdepsbioawk1.0.7
BWK awk modified for biological data1 rdepsbiococoa2.2.2_9
Bioinformatics framework1 rdepsbiosoup0.11.0_1
Collection of C++ header-only data structures for bioinformatics1 rdepsbtllib1.7.5_1
Bioinformatics Technology Lab common code library1 rdepsclustal-omega1.2.4
Multiple alignment of nucleic acid and protein, replaces clustalw1 rdepsclustalw2.1_3
Multiple alignment program for DNA or proteins1 rdepsemboss6.6.0_7
Collection of open source tools for genetic sequence analysis1 rdepserminej3.2
Analyses of gene sets such as gene expression profiling studies1 rdepsfastp0.26.0
Ultra-fast all-in-one FASTQ preprocessor1 rdepsfermi-lite0.1.13_2
Library and tool for assembling Illumina short reads in small regions1 rdepsflash1.2.11
Fast Length Adjustment of SHort reads1 rdepsgkl0.9.1
Accelerated kernel library for genomics1 rdepshaplohseq0.1.2.3_2
Identify regions of allelic imbalance1 rdepshmmer3.4
Profile hidden Markov models for biological sequence analysis1 rdepsigv2.16.0_1
Visualization tool for genomic datasets1 rdepsinfernal1.1.5
Search sequence databases for structural RNA homologs1 rdepsio_lib1.14.10_1
General purpose trace file (and Experiment File) reading interface1 rdepslibgtextutils0.7
Gordon's text utilities1 rdepslibsedml2.0.33_1
C++ SED-ML library1 rdepsmafft7.267_1
Multiple alignment program for amino acid or nucleotide sequences1 rdepsminimap22.30
Pairwise aligner for genomic and spliced nucleotide sequences1 rdepsmummer4.0.1
Modular system for rapid whole genome alignment1 rdepsncbi-blast+2.17.0
NCBI implementation of Basic Local Alignment Search Tool1 rdepsncbi-entrez-direct14.9.20210423_38
Access to the NCBI's suite of interconnected databases1 rdepsp5-Bio-ASN1-EntrezGene1.73_2,1
Regular expression-based Perl Parser for NCBI Entrez Gene1 rdepsp5-Bio-Coordinate1.007001
Modules for working with biological coordinates1 rdepsp5-Bio-FeatureIO1.6.905
Handler for FeatureIO1 rdepsp5-Bio-SCF1.03_2
Read and Update SCF Chromatographic Sequence Files1 rdepsp5-Bio-Variation1.7.5
BioPerl variation-related functionality1 rdepspear-merger0.9.6_1
Memory-efficient and highly accurate paired-end read merger1 rdepspicard-tools2.22.9
CLI tools for manipulating high-throughput sequencing (HTS) data1 rdepspy311-bcbio-gff0.7.1_1
Read and write Generic Feature Format (GFF) with Biopython integration1 rdepspy311-biom-format2.1.16_1
Biological Observation Matrix (BIOM) Format Project1 rdepspy311-bx-python0.14.0
Python module for reading, manipulating and writing genomic data sets1 rdepspy311-crossmap0.7.3_1
Lift over genomics coordinates between assemblies1 rdepspy311-deepTools3.5.2_2
User-friendly tools for exploring deep-sequencing data1 rdepspy311-deeptoolsintervals0.1.9_1
Python interface for deepTools interval trees1 rdepspy311-dnaio1.2.4
Read and write FASTQ and FASTA1 rdepspy311-goatools1.1.6_2
Tools for processing and visualizing Gene Ontology terms1 rdepspy311-mrcfile1.5.3_1
MRC file I/O library which is used in structural biology1 rdepspy311-newick1.10.0
Python module to read and write the Newick format1 rdepspy311-ont-fast5-api4.0.2_2
Interface to HDF5 files in Oxford Nanopore .fast5 format1 rdepspy311-py2bit0.3.0_1
Python interface for 2bit packed nucleotide files1 rdepspy311-pyfaidx0.5.9.5_1
Efficient pythonic random access to fasta subsequences1 rdepspy311-python-libsbml5.20.4_1
LibSBML Python API1 rdepspy311-valerius0.2_1
Python bioinformatics tools1 rdepsrainbow2.0.4
Efficient clustering and assembling of short reads, especially for RAD1 rdepsreadseq2.1.19
Read and reformat biosequences, Java command-line version1 rdepsrna-STAR2.7.11.a_1
Spliced Transcripts Alignment to a Reference1 rdepsrubygem-bio-old-biofetch-emulator1.0.0
Emulate Bio::Fetch object1 rdepssam2pairwise1.0.0
Show pairwise alignment for each read in a SAM file1 rdepsseqkit2.11.0_4
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation1 rdepsstacks2.68
Software pipeline for building loci from short-read sequences1 rdepsstringtie2.1.1
Transcript assembly and quantification for RNA-seq1 rdepssubread2.1.0
High-performance read alignment, quantification and mutation discovery1 rdepstrimadap0.1.4
Trim adapter sequences from Illumina data using heuristic rules1 rdepsucsc-userapps474
Command line tools from the UCSC Genome Browser project1 rdepsvcf-split0.1.5.10_1
Split a multi-sample VCF into single-sample VCFs1 rdepsvcf2hap0.1.6.7_1
Generate .hap file from VCF for haplohseq1 rdepsvcflib1.0.13
C++ library and CLI tools for parsing and manipulating VCF files1 rdepsvcftools0.1.17
Tools for working with VCF genomics files1 rdepsvt0.57721_3
Discovers short variants from Next Generation Sequencing data1 rdepswfa2-lib2.3.5
Exact gap-affine algorithm using homology to accelerate alignment1 rdepsFastTree2.1.11
Approximately-maximum-likelihood phylogenetic trees from alignmentsGroopM0.3.4_6
Metagenomic binning suiteMMseqs217.b804.f
Ultra fast and sensitive sequence search and clustering suiteabyss2.3.10
Assembly By Short Sequences: parallel, paired-end sequence assemblerandi0.14.3
Efficient estimation of evolutionary distancesartemis17.0.1.11
DNA sequence viewer and annotation toolatac-seq0.2.0_1
Metaport for ATAC-Seq analysisaugustus-gene-prediction3.5.0_16
Genome annotation toolavida2.12.4
Auto-adaptive genetic system designed for ALife researchbabel1.6_4
Converts among various molecular file formatsbarrnap0.9
BAsic Rapid Ribosomal RNA Predictorbcf-score1.20_3
Bcftools plugins for GWAS-VCF summary statistics filesbifrost1.3.5_1
Parallel construction, indexing and querying of de Bruijn graphsbioparser3.1.0
C++ header-only parsing library for several formats in bioinformaticsbiostar-tools2.1
Meta-port for Biostar Handbook toolsbolt-lmm2.3.6_17
Mixed model association testing and variance component analysisbowtie1.3.1
Ultrafast, memory-efficient short read alignercanu2.2_8
Single molecule sequence assemblercdbfasta2023.07.10
Fast indexing and retrieval of FASTA records from flat file databaseschip-seq0.1.2_1
Metaport for ChIP-Seq analysiscoverm0.7.0_11
Read coverage calculator for metagenomicscufflinks2.2.1.89_13
Cufflinks assembles transcripts, estimates their abundance, etccytoscape3.6.1
Software to visualize molecular interaction networks, gene expressiondDocent2.7.8_2
Bash pipeline for RAD sequencingdiamond2.1.16
BLAST-compatible local sequence alignerdsr-pdb1.0.3_17
Simple C++ PDB reader (reads the protein description format)edlib1.2.7
Fast C++ library for sequence alignment using edit distanceexonerate2.4.0_1
Generic tool for sequence alignmentfasda-utils0.1.0.2_1
Fast and simple differential analysis extrasfasta21.1.1_1
Collection of programs for searching DNA and protein databasesfasta336.3.8_1
Collection of programs for searching DNA and protein databasesfastahack1.0.0
Utility for indexing and sequence extraction from FASTA filesfastani1.34
Fast Whole-Genome Similarity (ANI) Estimationfastdnaml1.2.2_2
Faster DNAML, makes phylogenetic trees using maximum likelihoodfastool0.1.4
Simple and quick FastQ and FastA tool for file reading and conversionfastx_toolkit0.0.14_1
CLI tools for Short-Reads FASTA/FASTQ files preprocessingfigtree1.4.4.14
Graphical viewer of phylogenetic treesfluctuate1.40
Program to fit population modelsgarlic1.6_1
Molecular viewer, editor, and visualization programgatk4.6.2.0
Genome Analysis Toolkitgcta1.94.1_3
Genome-wide Complex Trait Analysisgemma0.98.5_1
Genome-wide Efficient Mixed Model Associationgenerand0.1.2_1
Generate random genomic data in FASTA/FASTQ, SAM, or VCF formatgff2ps0.98l
Convert gff-formatted genomic data sets to PostScriptgmap2020.09.12
Genomic Mapping and Alignment Program for mRNA and EST SequencesShowing 150 of 250 packages. Use the filter to narrow down.