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Bioinformatics and biology research tools

250 packages

This page covers abyss–preseq. 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.

Most Popular

htslib1.22C library for high-throughput sequencing data formats17 rdeps p5-BioPerl1.007008Collection of Perl modules for bioinformatics11 rdeps samtools1.22Tools for manipulating next-generation sequencing data10 rdeps biolibc0.2.7Low-level high-performance bioinformatics library7 rdeps bcftools1.22Tools for manipulating next-generation sequencing data5 rdeps

All Packages

150 results

Assembly By Short Sequences: parallel, paired-end sequence assembler

Add allelic depth info from a SAM stream to a VCF file1 rdeps

Efficient estimation of evolutionary distances

artemis17.0.1.11

DNA sequence viewer and annotation tool

atac-seq0.2.0_1

Metaport for ATAC-Seq analysis

augustus-gene-prediction3.5.0_16

Genome annotation tool

Auto-adaptive genetic system designed for ALife research

Converts among various molecular file formats

API and toolkit for handling BAM files3 rdeps

Utilities for working with SAM/BAM files1 rdeps

BAsic Rapid Ribosomal RNA Predictor

BBMap short read aligner, and other bioinformatic tools1 rdeps

bcf-score1.20_3

Bcftools plugins for GWAS-VCF summary statistics files

Tools for manipulating next-generation sequencing data5 rdeps

Toolset for genome set arithmetic such as intersect, union5 rdeps

Correct sequencing errors from Illumina sequencing data1 rdeps

Parallel construction, indexing and querying of de Bruijn graphs

bio-mocha1.20_1

Bcftools plugin for mosaic chromosomal alteration analysis1 rdeps

BWK awk modified for biological data1 rdeps

biococoa2.2.2_9

Bioinformatics framework1 rdeps

Low-level high-performance bioinformatics library7 rdeps

biolibc-tools0.1.5

High-performance bioinformatics tools based on biolibc3 rdeps

C++ header-only parsing library for several formats in bioinformatics

Library for reading and writing different biosignal data format3 rdeps

biosoup0.11.0_1

Collection of C++ header-only data structures for bioinformatics1 rdeps

biostar-tools2.1

Meta-port for Biostar Handbook tools

bolt-lmm2.3.6_17

Mixed model association testing and variance component analysis

Ultrafast, memory-efficient short read aligner

Ultrafast, memory-efficient short read aligner3 rdeps

Bioinformatics Technology Lab common code library1 rdeps

Burrows-Wheeler sequence aligner4 rdeps

Single molecule sequence assembler

Clustering and comparing protein or nucleotide sequences3 rdeps

cdbfasta2023.07.10

Fast indexing and retrieval of FASTA records from flat file databases

chip-seq0.1.2_1

Metaport for ChIP-Seq analysis

clustal-omega1.2.4

Multiple alignment of nucleic acid and protein, replaces clustalw1 rdeps

Multiple alignment program for DNA or proteins1 rdeps

Read coverage calculator for metagenomics

cufflinks2.2.1.89_13

Cufflinks assembles transcripts, estimates their abundance, etc

Software to visualize molecular interaction networks, gene expression

Bash pipeline for RAD sequencing

BLAST-compatible local sequence aligner

dsr-pdb1.0.3_17

Simple C++ PDB reader (reads the protein description format)

Fast C++ library for sequence alignment using edit distance

Collection of open source tools for genetic sequence analysis1 rdeps

Analyses of gene sets such as gene expression profiling studies1 rdeps

exonerate2.4.0_1

Generic tool for sequence alignment

Fast and simple differential analysis3 rdeps

fasda-utils0.1.0.2_1

Fast and simple differential analysis extras

Collection of programs for searching DNA and protein databases

Collection of programs for searching DNA and protein databases

Utility for indexing and sequence extraction from FASTA files

Fast Whole-Genome Similarity (ANI) Estimation

fastdnaml1.2.2_2

Faster DNAML, makes phylogenetic trees using maximum likelihood

Simple and quick FastQ and FastA tool for file reading and conversion

Ultra-fast all-in-one FASTQ preprocessor1 rdeps

fastq-trim0.1.4

Lightening fast sequence read trimmer3 rdeps

Quality control tool for high throughput sequence data5 rdeps

Approximately-maximum-likelihood phylogenetic trees from alignments

fastx_toolkit0.0.14_1

CLI tools for Short-Reads FASTA/FASTQ files preprocessing

fermi-lite0.1.13_2

Library and tool for assembling Illumina short reads in small regions1 rdeps

figtree1.4.4.14

Graphical viewer of phylogenetic trees

Fast Length Adjustment of SHort reads1 rdeps

Program to fit population models

Bayesian haplotype-based polymorphism discovery and genotyping2 rdeps

Molecular viewer, editor, and visualization program

Genome Analysis Toolkit

Genome-wide Complex Trait Analysis

Genome-wide Efficient Mixed Model Association

generand0.1.2_1

Generate random genomic data in FASTA/FASTQ, SAM, or VCF format

Convert gff-formatted genomic data sets to PostScript

GFF/GTF format conversions, filtering, FASTA extraction, etc2 rdeps

Accelerated kernel library for genomics1 rdeps

Genomic Mapping and Alignment Program for mRNA and EST Sequences

gperiodic3.0.3_1

Displays a periodic table of the elements

graphlan1.1.3_1

High-quality circular representations of taxonomic, phylogenetic trees

Metagenomic binning suite

haplohseq0.1.2.3_2

Identify regions of allelic imbalance1 rdeps

Remote protein homology detection suite

Alignment program for mapping next-generation sequencing reads2 rdeps

Profile hidden Markov models for biological sequence analysis1 rdeps

C library for high-throughput sequencing data formats17 rdeps

Hypothesis testing using Phylogenies

Visualization tool for genomic datasets1 rdeps

Search sequence databases for structural RNA homologs1 rdeps

io_lib1.14.10_1

General purpose trace file (and Experiment File) reading interface1 rdeps

Efficient phylogenomic software by maximum likelihood

jalview2.11.2.5

Viewer and editor for multiple sequence alignments

Jellyfish2.3.0_4

Fast, memory-efficient counting of k-mers in DNA1 rdeps

kallisto0.51.1_1,1

Quantify abundances of transcripts from RNA-Seq data2 rdeps

Accurate metagenomic profiling & fast large-scale genome searching

lamarc2.1.8_2,1

Package of programs for computing population parameters

C library for handling bigWig files (containing genomic data)

libcombine0.2.20_1

C++ library for working with the COMBINE archive format

GFF/GTF parsing library based on GCLib

libgtextutils0.7

Gordon's text utilities1 rdeps

libneurosim1.2.0_1

Common interfaces for neuronal simulators

C++ library for Numerical Markup Language3 rdeps

libsbml5.20.5_1

API Library for Working with SBML File4 rdeps

libsedml2.0.33_1

C++ SED-ML library1 rdeps

LocARNA provides several tools for the structural analysis of RNA

Multiple alignment program for amino acid or nucleotide sequences1 rdeps

Constructs linkage maps of markers segregating in experimental crosses

Fast approximate aligner for long DNA sequences

mca-calling0.1.0

Core tools for Mosaic Chromosomal Alteration event calling

megahit1.2.9.20

Ultra-fast single-node large and complex metagenomics assembly

Gene discovery and annotation for large-scale eukaryotic metagenomics

Program to estimate population sizes and migration rates

Pairwise aligner for genomic and spliced nucleotide sequences1 rdeps

MMseqs217.b804.f

Ultra fast and sensitive sequence search and clustering suite

Display molecular orbitals and electron densities in 2D and 3D

Software for bioinformatics of the microbial ecology community

Bayesian inference of phylogeny

Modular system for rapid whole genome alignment1 rdeps

MUltiple Sequence Comparison by Log-Expectation

ncbi-blast+2.17.0

NCBI implementation of Basic Local Alignment Search Tool1 rdeps

ncbi-cxx-toolkit29.7.0

NCBI C++ Toolkit

ncbi-entrez-direct14.9.20210423_38

Access to the NCBI's suite of interconnected databases1 rdeps

ncbi-toolkit2017.01.06_9

NCBI development toolkit, including BLAST 2 and GenBank/Entrez support

Tools and libraries for using data in the INSDC Sequence Read Archives

p5-AcePerl1.92_5

Perl5 interface to the ACEDB genome database system

p5-Bio-ASN1-EntrezGene1.73_2,1

Regular expression-based Perl Parser for NCBI Entrez Gene1 rdeps

p5-Bio-Cluster1.7.3_1

BioPerl cluster modules2 rdeps

p5-Bio-Coordinate1.007001

Modules for working with biological coordinates1 rdeps

p5-Bio-Das1.17_4

Client-side library for Distributed Genome Annotation System

p5-Bio-Das-Lite2.11_1

Perl extension for the DAS (HTTP+XML) Protocol

p5-Bio-DB-EMBL1.7.4

Database object interface for EMBL entry retrieval

p5-Bio-DB-NCBIHelper1.7.8

Collection of routines useful for queries to NCBI databases

p5-Bio-FeatureIO1.6.905

Handler for FeatureIO1 rdeps

p5-Bio-GFF32.0_2

Fast low-level functions for parsing and formatting GFF3

p5-Bio-Glite0.10_2

Perl Interface to G-language

p5-Bio-Graphics2.40_2

Generate GD Images of Bio::Seq Objects

p5-Bio-MAGETAB1.31_2

Data model and utility API for the MAGE-TAB format

p5-Bio-NEXUS0.78_1

Object-oriented Perl API for the NEXUS file format

p5-Bio-Phylo2.0.1

Phylogenetic analysis using Perl

p5-Bio-SCF1.03_2

Read and Update SCF Chromatographic Sequence Files1 rdeps

p5-Bio-Variation1.7.5

BioPerl variation-related functionality1 rdeps

p5-BioPerl1.007008

Collection of Perl modules for bioinformatics11 rdeps

p5-BioPerl-Run1.007003

Wrapper modules for common bioinformatics tools

p5-transdecoder5.7.1

Identify candidate coding regions within transcript sequences

p5-TrimGalore0.6.10

Wrapper around Cutadapt and FastQC for adapter and quality trimming

Phylogenetic Analysis by Maximum Likelihood (PAML)

PacBio BAM C++ library, with SWIG bindings

peak-classifier0.1.4.13_2

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF2 rdeps

pear-merger0.9.6_1

Memory-efficient and highly accurate paired-end read merger1 rdeps

phyml3.3.20220408_1,1

Simple, fast, and accurate algorithm to estimate large phylogenies

picard-tools2.22.9

CLI tools for manipulating high-throughput sequencing (HTS) data1 rdeps

plink1.90.b6.17_5

Whole genome association analysis toolset

Optimise DNA sequencing primer-set combinations

Predict yield of distinct reads from a genomic library