biology
Bioinformatics and biology research tools
250 packages — Page 2
This page covers primer3–wise. Search all 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. We have 1 guide covering biology software on FreeBSD.
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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
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100 results
primer32.3.6
Primer3 helps to choose primers for PCR reactionsprodigal2.6.3.16
Protein-coding gene prediction for prokaryotic genomesprodigy-lig1.1.3_1
Prediction of protein-small molecule binding affinitiesprotomol2.0.3_16
OO, component based, framework for molecular dynamics (MD) simulationspsi881.0_17
Plotting wavefunctions (molecular orbitals) in 3Dpy311-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-biopython1.85_2
Collection of Python modules for bioinformatics4 rdepspy311-biosig2.6.1_1
Library for reading and writing different biosignal data formatpy311-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-cutadapt5.2
Trim adapters from high-throughput sequencing reads2 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-dna-features-viewer3.1.3_2
Python library to visualize DNA features, e.g. GenBank or Gff filespy311-dnaio1.2.4
Read and write FASTQ and FASTA1 rdepspy311-ete33.1.3_3
Framework for the analysis and visualization of treespy311-Genesis-PyAPI1.2.1_1
API for the Genesis platform for genetics information processingpy311-gffutils0.13_1
Work with GFF and GTF files in a flexible database frameworkpy311-goatools1.1.6_2
Tools for processing and visualizing Gene Ontology terms1 rdepspy311-gtfparse2.5.0_1
Parsing tools for GTF (gene transfer format) filespy311-hits0.1_1
Utilities for processing high-throughput sequencing experimentspy311-HTSeq2.0.9_2
Python library to facilitate programmatic analysis of sequence datapy311-libnuml1.1.7
Numerical Markup Language for Pythonpy311-libsedml2.0.33
SED-ML library for Pythonpy311-loompy3.0.7_2
Work with .loom files for single-cell RNA-seq datapy311-macs22.2.9.1_1
Identify transcription factor binding sites2 rdepspy311-MACS33.0.3
Peak caller aimed at transcription factor binding sitespy311-mrcfile1.5.3_1
MRC file I/O library which is used in structural biology1 rdepspy311-multiqc1.25.2_3
Aggregate bioinformatics analysis reports across samples and tools4 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-pandas-charm0.3.0_3
Library for getting character matrices into and out of pandaspy311-py2bit0.3.0_1
Python interface for 2bit packed nucleotide files1 rdepspy311-pyBigWig0.3.22_1
Python access to bigWig files using libBigWig2 rdepspy311-pydeseq20.5.2_1
Python implementation of the popular DESeq2 R packagepy311-pyfaidx0.5.9.5_1
Efficient pythonic random access to fasta subsequences1 rdepspy311-pyfasta0.5.2_6
Fast, memory-efficient, pythonic access to fasta sequence filespy311-pyrodigal3.6.3
Python binding for Prodigal, an ORF finder for genomes and metagenomespy311-pysam0.23.0_1
Python module for reading, manipulating and writing genomic data sets4 rdepspy311-pysces1.2.2_1
Python Simulator for Cellular Systemspy311-python-libsbml5.20.4_1
LibSBML Python API1 rdepspy311-python-nexus2.9.0_1
Generic nexus file format reader for pythonpy311-pywgsim0.5.2_2
Modified wgsim genomic data simulatorpy311-resdk22.0.0
Resolwe SDK to interact with Resolwe server and Resolwe Bioinformaticspy311-scikit-bio0.6.3_1
Data structures, algorithms, educational resources for bioinformaticspy311-valerius0.2_1
Python bioinformatics tools1 rdepspy311-xenaPython1.0.14_1
API for Xena Hub to access genetic information shared through the hubR-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 rdepsrainbow2.0.4
Efficient clustering and assembling of short reads, especially for RAD1 rdepsrampler2.0.0_1
Standalone module for sampling genomic sequencesreadseq2.1.19
Read and reformat biosequences, Java command-line version1 rdepsrna-seq0.1.4_1
Metaport for RNA-Seq analysisrna-STAR2.7.11.a_1
Spliced Transcripts Alignment to a Reference1 rdepsruby33-bio1.5.1
Integrated environment for Bioinformatics written in Rubyrubygem-bio2.0.6
Integrated environment for Bioinformatics written in Ruby3 rdepsrubygem-bio-executables1.0.0
Collection of miscellaneous utilities for bioinformaticsrubygem-bio-old-biofetch-emulator1.0.0
Emulate Bio::Fetch object1 rdepsrubygem-bio-shell1.0.1
Command-line interface on BioRubysalmon1.10.3_1
Transcript-level quantification of RNA-seq from lightweight alignmentssam2pairwise1.0.0
Show pairwise alignment for each read in a SAM file1 rdepssamtools1.22
Tools for manipulating next-generation sequencing data10 rdepsscrm1.7.4_1
Coalescent simulator for biological sequencesseaview5.1,1
Multiple DNA/protein sequence alignment editorseqan2.4.0
C++ sequence analysis template libraryseqan11.3.1_4
C++ Sequence Analysis Libraryseqan33.4.0
C++ header-only library for biological sequence analysisseqkit2.11.0_4
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation1 rdepsseqtk1.5
Tool for processing sequences in FASTA/FASTQ format2 rdepsseqwish0.7.11_2
Alignment to variation graph inducersigviewer0.6.4.13_2
Viewing application for biosignalsslclust2010.02.02
Single-linkage clustering with Jaccard similaritysmithwatermang20160702
Smith-waterman-gotoh alignment algorithmspoa4.1.5
C++ implementation of the partial order alignment (POA) algorithmsra-tools3.3.0_2
NCBI's toolkit for handling data in INSDC Sequence Read Archives5 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 rdepstabixpp1.1.2
C++ wrapper to tabix indexertaxonkit0.19.0_13
Practical and efficient NCBI taxonomy toolkittreekin0.5.1_7
Efficient computation of RNA folding dynamicstreepuzzle5.2
Maximum likelihood phylogeny reconstruction using quartetstrimadap0.1.4
Trim adapter sequences from Illumina data using heuristic rules1 rdepstrimmomatic0.39
Flexible read trimming tool for Illumina NGS data2 rdepstRNAscan-SE2.0.11
Searching for tRNA genes in genomic sequenceucsc-userapps474
Command line tools from the UCSC Genome Browser project1 rdepsugene40.1_1
Integrated bioinformatics toolkitunikmer0.20.0_17
Toolkit for nucleic acid k-mer analysis, set operations on k-mersvcf-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 rdepsvelvet1.2.10_2
Sequence assembler for very short readsviennarna2.7.0_2
Alignment tools for the structural analysis of RNAvsearch2.30.2
Versatile open-source tool for metagenomicsvt0.57721_3
Discovers short variants from Next Generation Sequencing data1 rdepswfa2-lib2.3.5
Exact gap-affine algorithm using homology to accelerate alignment1 rdepswise2.4.1_1
Intelligent algorithms for DNA searches