biology - The NetBSD Packages Collection
Software for the biological sciences
Here are the one-line descriptions for each of the
61
items in this directory:
- R-popbio-2.7
- Construction and Analysis of Matrix Population Models
- arka-0.11nb2
- Graphic interface for the programs from the GP package
- azara-2.7nb8
- Programs to process and view NMR data
- bcftools-1.10.2nb2
- Tools for manipulating BCF and VCF variant call files
- bedtools-2.30.0
- Swiss army knife for genome arithmetic
- bioperl-1.7.7
- Perl tools for computational molecular biology
- bodr-9nb12
- Blue Obelisk Data Repository
- bowtie2-2.4.2
- Ultrafast, memory-efficient short read aligner
- bwa-0.7.17nb4
- Map low-divergent sequences against a large reference genome
- canu-1.8nb8
- Single molecule sequence assembler for genomes large and small
- cdhit-4.6.4nb4
- Clustering and comparing protein or nucleotide sequences
- chemical-mime-data-0.1.94
- Chemical mime and file type support for desktops
- chemtool-1.6.14nb15
- Program for drawing organic molecules
- clustalw-2.1
- General purpose multiple alignment program for DNA or proteins
- coalesce-1.5.0.2nb1
- Estimates effective population size and mutation rate
- coordgenlibs-1.4.2nb1
- 2D coordinate generation for molecules
- fastDNAml-1.2.2
- Program derived from Joseph Felsenstein's version 3.3 DNAML
- fastp-0.20.0
- Ultra-fast all-in-one FASTQ preprocessor
- fastqc-0.11.9
- Quality control tool for high throughput sequence data
- fluctuate-1.4
- Estimation of population growth rate
- gabedit-2.4.8nb11
- Graphical User Interface to computational chemistry packages
- genesplicer-20030403
- Computational Method for Splice Site Prediction
- glimmer-2.13nb1
- System for finding genes in microbial DNA
- gnome-chemistry-utils-0.14.16nb4
- GChemPaint, a 2D chemical editor and other programs
- gp-0.26
- Manipulate DNA/RNA sequence in a Unix fashion
- gromacs-4.5.5nb11
- Molecular dynamics package
- hisat2-2.1.0.23nb4
- Alignment program for mapping next-generation sequencing reads
- hmmer-3.0
- Implementation of profile HMM software for protein sequence analysis
- htslib-1.10.2nb2
- C library for high-throughput sequencing data formats
- igv-2.9.2
- Visualization tool for genomic datasets
- kallisto-0.46.1
- Quantify abundances of transcripts from RNA-Seq data
- lucy-1.20
- Sequence Cleanup Program
- maeparser-1.2.4nb1
- Parser for Maestro file format
- molsketch-0.7.0
- Program for drawing molecular structures
- mopac-7.0nb1
- Molecular energy calculation program
- mpqc-2.3.1nb10
- The Massively Parallel Quantum Chemistry Program
- mummer-3.20nb8
- System for aligning whole genome sequences
- ncbi-blast+-2.8.1nb12
- NCBI implementation of Basic Local Alignment Search Tool
- nut-15.8
- Record what you eat and analyze your meals
- openbabel-3.1.1nb4
- Chemistry file translation program
- p5-Bio-ASN1-EntrezGene-1.73
- Regular expression-based Perl Parser for NCBI Entrez Gene
- pdbalign-20030812
- Prediction of Protein Secondary Structure and Active Sites
- phylip-3.69
- Phylogeny Inference Package
- plink-1.07nb1
- Whole-genome association analysis toolset
- plinkseq-0.08nb3
- C/C++ library for working with human genetic variation data
- primer3-2.3.6
- Design PCR primers
- profit-2.2nb1
- Performs least squares fits of two protein structures
- puzzle-5.2
- Maximum likelihood analysis of molecular sequence data
- py38-biopython-1.74nb1
- Python libraries for computational molecular biology
- py38-cutadapt-3.2
- Find and remove adapter sequences, primers, poly-A tails, etc
- py38-dnaio-0.5.0
- Read and write FASTQ and FASTA files
- py27-mol-1.5.0.1nb8
- Molecular Visualization System
- py38-pydicom-1.3.0
- Pure python package for working with DICOM files
- rasmol-2.7.3nb2
- Molecular Graphics Visualisation Tool
- samtools-1.10nb2
- Tools for manipulating sequence alignment maps
- sewer-2.6nb2
- SEquence Analysis using WEb Resources
- stacks-2.2nb4
- Software pipeline for building loci from short-read sequences
- stride-20030804
- Protein secondary structure assignment from atomic coordinates
- Trimmomatic-0.38
- Flexible read trimming tool for Illumina NGS data
- vsearch-2.13.4
- Versatile open-source tool for metagenomics
- xylem-1.8.7
- Tools for manipulation of genetic databases
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