biology - The NetBSD Packages Collection
Software for the biological sciences
There are
96
packages in this category:
- R-popbio-2.8
- Construction and Analysis of Matrix Population Models
- ad2vcf-0.1.6.20
- Add allelic depth info from a SAM stream to a VCF file
- arka-0.11nb2
- Graphic interface for the programs from the GP package
- atac-seq-1.5.0
- Core tools needed for ATAC-Seq analysis
- azara-2.7nb10
- Programs to process and view NMR data
- balance-tui-0.1.2
- Balance chemical equations from the CLI
- bcf-score-1.20
- Bcftools plugin for mosaic chromosomal alteration analysis
- bcftools-1.21
- Tools for manipulating BCF and VCF variant call files
- beagle-5.2
- Phasing genotypes and imputing ungenotyped markers
- bedtools-2.31.1
- Swiss army knife for genome arithmetic
- bio-mocha-1.20
- Bcftools plugin for mosaic chromosomal alteration analysis
- biolibc-0.2.6.4
- Low-level high-performance bioinformatics library
- biolibc-tools-0.1.4.13
- High-performance bioinformatics tools based on biolibc
- bioperl-1.7.7nb5
- Perl tools for computational molecular biology
- bodr-9nb25
- Blue Obelisk Data Repository
- bowtie2-2.5.4
- Ultrafast, memory-efficient short read aligner
- bwa-0.7.17nb7
- Map low-divergent sequences against a large reference genome
- canu-2.2nb6
- Single molecule sequence assembler for genomes large and small
- cdhit-4.8.1nb1
- Clustering and comparing protein or nucleotide sequences
- chemtool-1.6.14nb26
- Program for drawing organic molecules
- chip-seq-1.2
- Core tools needed for ChIP-Seq analysis
- 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-1.4.2nb9
- 2D coordinate generation for molecules
- fasda-0.1.5.8
- Fast and simple differential analysis
- fastDNAml-1.2.2
- Program derived from Joseph Felsenstein's version 3.3 DNAML
- fastp-0.22.0
- Ultra-fast all-in-one FASTQ preprocessor
- fastq-trim-0.1.3
- Lightening fast sequence read trimmer
- fastqc-0.11.9nb2
- Quality control tool for high throughput sequence data
- FastTree-2.1.11
- Approximately-maximum-likelihood phylogenetic trees from alignments
- fastx-toolkit-0.0.14.6nb1
- CLI tools for Short-Reads FASTA/FASTQ files preprocessing
- filter-fastq-0.0.0.20210527nb2
- Filter reads from a FASTQ file
- fluctuate-1.4
- Estimation of population growth rate
- gabedit-2.4.8nb22
- Graphical User Interface to computational chemistry packages
- generand-0.1.2.9
- Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
- genesplicer-20030403
- Computational Method for Splice Site Prediction
- gffread-0.12.7
- GFF/GTF format conversions, filtering, FASTA extraction, etc
- glimmer-2.13nb1
- System for finding genes in microbial DNA
- gp-0.26
- Manipulate DNA/RNA sequence in a Unix fashion
- gromacs-4.5.5nb25
- Molecular dynamics package
- haplohseq-0.1.2.2nb2
- Identify regions of allelic imbalance
- hisat2-2.2.1nb4
- Alignment program for mapping next-generation sequencing reads
- hmmer-3.0nb1
- Implementation of profile HMM software for protein sequence analysis
- htslib-1.21nb5
- C library for high-throughput sequencing data formats
- igv-2.9.2
- Visualization tool for genomic datasets
- kallisto-0.51.1
- Quantify abundances of transcripts from RNA-Seq data
- libpll-0.3.2nb1
- High-performance software library for phylogenetic analysis
- lucy-1.20
- Sequence Cleanup Program
- maeparser-1.2.4nb9
- Parser for Maestro file format
- mca-calling-0.1.0
- Core tools for Mosaic Chromosomal Alteration event calling
- microsynteny-tools-0.1.0.175
- Tools for exploring microsyntenic differences among species
- miniasm-0.3
- OLC-based de novo assembler for long reads
- minimap2-2.28nb1
- Sequence alignment program for noisy, long reads
- molsketch-0.8.1nb8
- Program for drawing molecular structures
- mopac-22.0.6nb1
- Semi-empirical (MNDO, etc.) molecular orbital calculation
- mpqc-2.3.1nb12
- The Massively Parallel Quantum Chemistry Program
- mummer-3.20nb10
- System for aligning whole genome sequences
- ncbi-blast+-2.16.0nb1
- NCBI implementation of Basic Local Alignment Search Tool
- nutsqlite-2.0.6
- Record what you eat and analyze your meals
- openbabel-3.1.1nb36
- Chemistry file translation program
- p5-Bio-ASN1-EntrezGene-1.73nb4
- Regular expression-based Perl Parser for NCBI Entrez Gene
- pdbalign-20030812
- Prediction of Protein Secondary Structure and Active Sites
- peak-classifier-0.1.4.21
- Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
- phylip-3.69
- Phylogeny Inference Package
- plink-1.07nb1
- Whole-genome association analysis toolset
- plinkseq-0.08nb14
- 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
- py312-bcbio-gff-0.7.1
- Read and write Generic Feature Format (GFF) with Biopython integration
- py312-biopython-1.85nb1
- Python libraries for computational molecular biology
- py312-cutadapt-4.7nb1
- Find and remove adapter sequences, primers, poly-A tails, etc
- py312-dna-features-viewer-3.1.3
- Python library to visualize DNA features, e.g. GenBank or Gff files
- py312-dnaio-1.2.0nb1
- Read and write FASTQ and FASTA files
- py312-macs2-2.2.9.1nb2
- Algorithm for identifying transcription factor binding sites
- py312-macs3-3.0.2nb2
- Peak caller aimed at transcription factor binding sites
- py312-multiqc-1.25.2nb1
- Aggregate bioinformatics analysis reports across samples and tools
- py312-pydicom-2.4.4nb1
- Pure python package for working with DICOM files
- racon-1.4.3
- Genomic consensus builder
- rasmol-2.7.3nb2
- Molecular Graphics Visualisation Tool
- rna-seq-1.3.0
- Core tools needed for RNA-Seq analysis
- rna-star-2.7.10b
- Spliced Transcripts Alignment to a Reference
- samtools-1.21
- Tools for manipulating sequence alignment maps
- seqtk-1.4
- Tool for processing sequences in FASTA/FASTQ format
- sewer-2.6nb2
- SEquence Analysis using WEb Resources
- sra-tools-3.2.0nb1
- NCBI's toolkit for handling data in INSDC Sequence Read Archives
- stacks-2.68
- Software pipeline for building loci from short-read sequences
- stride-20030804
- Protein secondary structure assignment from atomic coordinates
- stringtie-2.1.1
- Transcript assembly and quantification for RNA-seq
- subread-2.0.8
- High-performance read alignment, quantification and mutation discovery
- Trimmomatic-0.38
- Flexible read trimming tool for Illumina NGS data
- vcf-split-0.1.5.19
- Split a multi-sample VCF into single-sample VCFs
- vcf2hap-0.1.6.14
- Generate .hap file from VCF for haplohseq
- vsearch-2.29.4
- Versatile open-source tool for metagenomics
- xmakemol-5.16h
- Program for visualizing atomic and molecular systems
- xylem-1.8.7
- Tools for manipulation of genetic databases