BSD Portsbiology 303 NetBSD ports
Biology-related software
| Port | Version | Repository | Comment |
|---|---|---|---|
| biology/R-popbio | 2.8 | pkgsrc | Construction and Analysis of Matrix Population Models |
| biology/ad2vcf | 0.1.6.20 | pkgsrc | Add allelic depth info from a SAM stream to a VCF file |
| biology/arka | 0.11nb2 | pkgsrc | Graphic interface for the programs from the GP package |
| biology/atac-seq | 1.5.0 | pkgsrc | Core tools needed for ATAC-Seq analysis |
| biology/azara | 2.7nb10 | pkgsrc | Programs to process and view NMR data |
| biology/balance-tui | 0.1.2 | pkgsrc | Balance chemical equations from the CLI |
| biology/bcf-score | 1.20nb1 | pkgsrc | Bcftools plugin for mosaic chromosomal alteration analysis |
| biology/bcftools | 1.21 | pkgsrc | Tools for manipulating BCF and VCF variant call files |
| biology/beagle | 5.2 | pkgsrc | Phasing genotypes and imputing ungenotyped markers |
| biology/bedtools | 2.31.1 | pkgsrc | Swiss army knife for genome arithmetic |
| biology/bio-mocha | 1.20 | pkgsrc | Bcftools plugin for mosaic chromosomal alteration analysis |
| biology/biolibc | 0.2.6.4 | pkgsrc | Low-level high-performance bioinformatics library |
| biology/biolibc-tools | 0.1.4.13 | pkgsrc | High-performance bioinformatics tools based on biolibc |
| biology/bioperl | 1.7.7nb7 | pkgsrc | Perl tools for computational molecular biology |
| biology/bodr | 9nb26 | pkgsrc | Blue Obelisk Data Repository |
| biology/bowtie2 | 2.5.4 | pkgsrc | Ultrafast, memory-efficient short read aligner |
| biology/bwa | 0.7.17nb7 | pkgsrc | Map low-divergent sequences against a large reference genome |
| biology/canu | 2.2nb11 | pkgsrc | Single molecule sequence assembler for genomes large and small |
| biology/cdhit | 4.8.1nb1 | pkgsrc | Clustering and comparing protein or nucleotide sequences |
| biology/chemtool | 1.6.14nb31 | pkgsrc | Program for drawing organic molecules |
| biology/chip-seq | 1.2 | pkgsrc | Core tools needed for ChIP-Seq analysis |
| biology/clustalw | 2.1 | pkgsrc | General purpose multiple alignment program for DNA or proteins |
| biology/coalesce | 1.5.0.2nb1 | pkgsrc | Estimates effective population size and mutation rate |
| biology/coordgenlibs | 1.4.2nb12 | pkgsrc | 2D coordinate generation for molecules |
| biology/fasda | 0.1.5.8 | pkgsrc | Fast and simple differential analysis |
| biology/fastDNAml | 1.2.2 | pkgsrc | Program derived from Joseph Felsenstein's version 3.3 DNAML |
| biology/fastp | 0.22.0 | pkgsrc | Ultra-fast all-in-one FASTQ preprocessor |
| biology/fastq-trim | 0.1.3 | pkgsrc | Lightening fast sequence read trimmer |
| biology/fastqc | 0.11.9nb2 | pkgsrc | Quality control tool for high throughput sequence data |
| biology/fasttree | 2.1.11 | pkgsrc | Approximately-maximum-likelihood phylogenetic trees from alignments |
| biology/fastx-toolkit | 0.0.14.6nb1 | pkgsrc | CLI tools for Short-Reads FASTA/FASTQ files preprocessing |
| biology/filter-fastq | 0.0.0.20210527nb2 | pkgsrc | Filter reads from a FASTQ file |
| biology/fluctuate | 1.4 | pkgsrc | Estimation of population growth rate |
| biology/gabedit | 2.4.8nb26 | pkgsrc | Graphical User Interface to computational chemistry packages |
| biology/generand | 0.1.2.9 | pkgsrc | Generate random genomic data in FASTA/FASTQ, SAM, or VCF format |
| biology/genesplicer | 20030403 | pkgsrc | Computational Method for Splice Site Prediction |
| biology/gffread | 0.12.7 | pkgsrc | GFF/GTF format conversions, filtering, FASTA extraction, etc |
| biology/glimmer | 2.13nb1 | pkgsrc | System for finding genes in microbial DNA |
| biology/gp | 0.26 | pkgsrc | Manipulate DNA/RNA sequence in a Unix fashion |
| biology/gromacs | 4.5.5nb26 | pkgsrc | Molecular dynamics package |
| biology/hisat2 | 2.2.1nb4 | pkgsrc | Alignment program for mapping next-generation sequencing reads |
| biology/hmmer | 3.0nb1 | pkgsrc | Implementation of profile HMM software for protein sequence analysis |
| biology/htslib | 1.21nb9 | pkgsrc | C library for high-throughput sequencing data formats |
| biology/igv | 2.9.2 | pkgsrc | Visualization tool for genomic datasets |
| biology/kallisto | 0.51.1 | pkgsrc | Quantify abundances of transcripts from RNA-Seq data |
| biology/lucy | 1.20 | pkgsrc | Sequence Cleanup Program |
| biology/maeparser | 1.3.2nb3 | pkgsrc | Parser for Maestro file format |
| biology/microsynteny-tools | 0.1.0.175 | pkgsrc | Tools for exploring microsyntenic differences among species |
| biology/miniasm | 0.3 | pkgsrc | OLC-based de novo assembler for long reads |
| biology/minimap2 | 2.28nb1 | pkgsrc | Sequence alignment program for noisy, long reads |
| biology/molsketch | 0.8.4nb7 | pkgsrc | Program for drawing molecular structures |
| biology/mopac | 22.0.6nb1 | pkgsrc | Semi-empirical (MNDO, etc.) molecular orbital calculation |
| biology/mpqc | 2.3.1nb12 | pkgsrc | The Massively Parallel Quantum Chemistry Program |
| biology/mummer | 3.20nb10 | pkgsrc | System for aligning whole genome sequences |
| biology/ncbi-blast+ | 2.16.0nb4 | pkgsrc | NCBI implementation of Basic Local Alignment Search Tool |
| biology/nutsqlite | 2.0.6 | pkgsrc | Record what you eat and analyze your meals |
| biology/openbabel | 3.2.1nb2 | pkgsrc | Chemistry file translation program |
| biology/p5-Bio-ASN1-EntrezGene | 1.73nb6 | pkgsrc | Regular expression-based Perl Parser for NCBI Entrez Gene |
| biology/pdbalign | 20030812 | pkgsrc | Prediction of Protein Secondary Structure and Active Sites |
| biology/peak-classifier | 0.1.4.21 | pkgsrc | Classify ChIP/ATAC-Seq peaks based on features provided in a GFF |
| biology/phylip | 3.69 | pkgsrc | Phylogeny Inference Package |
| biology/plink | 1.07nb1 | pkgsrc | Whole-genome association analysis toolset |
| biology/plinkseq | 0.08nb19 | pkgsrc | C/C++ library for working with human genetic variation data |
| biology/primer3 | 2.3.6 | pkgsrc | Design PCR primers |
| biology/profit | 2.2nb1 | pkgsrc | Performs least squares fits of two protein structures |
| biology/puzzle | 5.2nb2 | pkgsrc | Maximum likelihood analysis of molecular sequence data |
| biology/py-bcbio-gff | 0.7.1 | pkgsrc | Read and write Generic Feature Format (GFF) with Biopython integration |
| biology/py-biopython | 1.87 | pkgsrc | Python libraries for computational molecular biology |
| biology/py-cutadapt | 4.7nb1 | pkgsrc | Find and remove adapter sequences, primers, poly-A tails, etc |
| biology/py-dna-features-viewer | 3.1.5 | pkgsrc | Python library to visualize DNA features, e.g. GenBank or Gff files |
| biology/py-dnaio | 1.2.0nb1 | pkgsrc | Read and write FASTQ and FASTA files |
| biology/py-macs2 | 2.2.9.1nb3 | pkgsrc | Algorithm for identifying transcription factor binding sites |
| biology/py-macs3 | 3.0.2nb2 | pkgsrc | Peak caller aimed at transcription factor binding sites |
| biology/py-multiqc | 1.25.2nb1 | pkgsrc | Aggregate bioinformatics analysis reports across samples and tools |
| biology/py-pydicom | 3.0.2 | pkgsrc | Pure python package for working with DICOM files |
| biology/racon | 1.4.3 | pkgsrc | Genomic consensus builder |
| biology/rasmol | 2.7.3nb2 | pkgsrc | Molecular Graphics Visualisation Tool |
| biology/rna-seq | 1.3.0 | pkgsrc | Core tools needed for RNA-Seq analysis |
| biology/rna-star | 2.7.10b | pkgsrc | Spliced Transcripts Alignment to a Reference |
| biology/samtools | 1.21 | pkgsrc | Tools for manipulating sequence alignment maps |
| biology/seqtk | 1.4 | pkgsrc | Tool for processing sequences in FASTA/FASTQ format |
| biology/sewer | 2.6nb2 | pkgsrc | SEquence Analysis using WEb Resources |
| biology/sra-tools | 3.2.0nb2 | pkgsrc | NCBI's toolkit for handling data in INSDC Sequence Read Archives |
| biology/stacks | 2.68 | pkgsrc | Software pipeline for building loci from short-read sequences |
| biology/stride | 20030804 | pkgsrc | Protein secondary structure assignment from atomic coordinates |
| biology/stringtie | 2.1.1 | pkgsrc | Transcript assembly and quantification for RNA-seq |
| biology/trimmomatic | 0.38 | pkgsrc | Flexible read trimming tool for Illumina NGS data |
| biology/vcf-split | 0.1.5.19 | pkgsrc | Split a multi-sample VCF into single-sample VCFs |
| biology/vcf2hap | 0.1.6.14 | pkgsrc | Generate .hap file from VCF for haplohseq |
| biology/vsearch | 2.29.4 | pkgsrc | Versatile open-source tool for metagenomics |
| biology/xmakemol | 5.16h | pkgsrc | Program for visualizing atomic and molecular systems |
| biology/xylem | 1.8.7 | pkgsrc | Tools for manipulation of genetic databases |
| wip/ARC | 1.1.4 | pkgsrc-wip | Genomics pipeline for de novo assemblies |
| wip/GSAlign | 1.0.22 | pkgsrc-wip | Ultra-fast intra-species sequence alignment |
| wip/GenericRepeatFinder | 1.0 | pkgsrc-wip | Detect repeated sequences in genomes |
| wip/SNAP | 0.0.0.20210910 | pkgsrc-wip | Gene finding for prokaryotic and eukaryotic genomes |
| wip/ad2vcf | 0.1.6.20 | pkgsrc-wip | Add allelic depth info from a SAM stream to a VCF file |
| wip/artemis | 6nb2 | pkgsrc-wip | Genome viewer and annotation too |
| wip/atac-seq | 1.5.0 | pkgsrc-wip | Core tools needed for ATAC-Seq analysis |
| wip/bamtools | 2.5.3 | pkgsrc-wip | API and toolkit for handling BAM files |
| wip/bcf-score | 1.20 | pkgsrc-wip | Bcftools plugin for mosaic chromosomal alteration analysis |
| wip/bcftools | 1.22 | pkgsrc-wip | Tools for manipulating BCF and VCF variant call files |
| wip/bedtools | 2.31.1 | pkgsrc-wip | Swiss army knife for genome arithmetic |
| wip/bifrost | 1.3.5nb1 | pkgsrc-wip | Parallel construction, indexing and querying of de Bruijn graphs |
| wip/bio-mocha | 1.20 | pkgsrc-wip | Bcftools plugin for mosaic chromosomal alteration analysis |
| wip/biolibc | 0.2.7 | pkgsrc-wip | Low-level high-performance bioinformatics library |
| wip/biolibc-tools | 0.1.5 | pkgsrc-wip | High-performance bioinformatics tools based on biolibc |
| wip/bioruby | 0.6.2nb1 | pkgsrc-wip | Intergrated environment for Bioinformatics using Ruby |
| wip/biostar-tools | 1.10.1 | pkgsrc-wip | Meta-package for Biostar Handbook tools |
| wip/blast2go | 2.3.5 | pkgsrc-wip | GO annotation and functional genome analysis |
| wip/bolt-lmm | 2.3.2nb1 | pkgsrc-wip | Statistics for testing association between phenotype and genotypes |
| wip/bowtie2 | 2.5.4 | pkgsrc-wip | Ultrafast, memory-efficient short read aligner |
| wip/bpcscripts | 2016.02.09 | pkgsrc-wip | Gast Illumina processing |
| wip/brain-mesh-builder | 1.1 | pkgsrc-wip | Surface mesh building based on 3-dimensional image stacks |
| wip/bwa | 0.7.17nb7 | pkgsrc-wip | Map low-divergent sequences against a large reference genome |
| wip/canu | 2.2 | pkgsrc-wip | Single molecule sequence assembler for genomes large and small |
| wip/centrifuge | 1.0.4 | pkgsrc-wip | Novel microbial classification engine |
| wip/chemeq | 2.12 | pkgsrc-wip | Chemical Equation Parser and Renderer |
| wip/chip-seq | 1.2 | pkgsrc-wip | Core tools needed for ChIP-Seq analysis |
| wip/cortex-var | 1.0.5.21 | pkgsrc-wip | TODO: Short description of the package |
| wip/cropsr | 0.0.0.44 | pkgsrc-wip | Complex genome-wide CRISPR gRNA design and validation |
| wip/cufflinks | 2.1.1 | pkgsrc-wip | Transcript assembly, differential expression, regulation for RNA-Seq |
| wip/cufflinks-2.2.1 | 2.2.1 | pkgsrc-wip | RNA transcript assembly, differential expression/regulation |
| wip/ddocent | 2.5.2 | pkgsrc-wip | Bash pipeline for RAD sequencing |
| wip/dfam | 3.5 | pkgsrc-wip | Collection of genome annotation data |
| wip/epacts | 2017.08.15 | pkgsrc-wip | Efficient and Parallelizable Association Container Toolbox |
| wip/etos | 3.1.4nb1 | pkgsrc-wip | Efficient technology of spike-sorting |
| wip/exonerate | 2.2.0 | pkgsrc-wip | Generic tool for pairwise sequence comparison |
| wip/famsa | 1.2.4 | pkgsrc-wip | Algorithm for large-scale multiple sequence alignments |
| wip/fasda | 0.2.0.1 | pkgsrc-wip | Fast and simple differential analysis |
| wip/fasda-utils | 0.1.0.5 | pkgsrc-wip | Fast and simple differential analysis extras |
| wip/fasta | 36.3.5.4 | pkgsrc-wip | FASTA sequence comparison programs |
| wip/fastahack | 0.0.0.20160702 | pkgsrc-wip | Utilities for indexing and sequence extraction from FASTA files |
| wip/fastaunique | 2016.02.08 | pkgsrc-wip | Sort and uniq fasta files |
| wip/fastool | 0.1.4 | pkgsrc-wip | Simple and quick FastQ and FastA tool for file reading and conversion |
| wip/fastp | 1.0.1 | pkgsrc-wip | Ultra-fast all-in-one FASTQ preprocessor |
| wip/fastq-trim | 0.1.4 | pkgsrc-wip | Lightening fast sequence read trimmer |
| wip/fastqc | 0.11.9nb2 | pkgsrc-wip | Quality control tool for high throughput sequence data |
| wip/fasttree | 2.1.11 | pkgsrc-wip | Approximately-maximum-likelihood phylogenetic trees from alignments |
| wip/fastx-toolkit | 0.0.14.6nb1 | pkgsrc-wip | CLI tools for Short-Reads FASTA/FASTQ files preprocessing |
| wip/gcta | 1.94.1 | pkgsrc-wip | Genome-wide Complex Trait Analysis |
| wip/gemma | 0.98.5 | pkgsrc-wip | Genome-wide Efficient Mixed Model Association |
| wip/generand | 0.1.2.9 | pkgsrc-wip | Generate random genomic data in FASTA/FASTQ, SAM, or VCF format |
| wip/genometools | 1.6.2 | pkgsrc-wip | Collection of bioinformatics tools |
| wip/gffread | 0.12.7 | pkgsrc-wip | GFF/GTF format conversions, filtering, FASTA extraction, etc |
| wip/glimmerm | 2.5.1 | pkgsrc-wip | Gene finder developed specifically for eukaryotes |
| wip/gmap | 2014.07.04 | pkgsrc-wip | Genomic Mapping and Alignment Program for mRNA and EST Sequences |
| wip/haplohseq | 0.1.2.5 | pkgsrc-wip | Identify regions of allelic imbalance |
| wip/hisat2 | 2.2.1nb2 | pkgsrc-wip | Alignment program for mapping next-generation sequencing reads |
| wip/htslib | 1.22 | pkgsrc-wip | C library for high-throughput sequencing data formats |
| wip/igv | pkgsrc-wip | Visualization tool for genomic datasets | |
| wip/jalview | 1.8 | pkgsrc-wip | Jalview is a multiple alignment editor written in java |
| wip/jellyfish | 1.1.11 | pkgsrc-wip | Fast, memory-efficient counting of k-mers in DNA |
| wip/jellyfish2 | 2.2.10 | pkgsrc-wip | Fast, memory-efficient counting of k-mers in DNA |
| wip/jemboss-standalone | 2.9.0nb1 | pkgsrc-wip | Standalone Interface for EMBOSS |
| wip/jmol | binary | pkgsrc-wip | Jmol: an open-source Java viewer for chemical structures in 3D |
| wip/kallisto | 0.51.1nb1 | pkgsrc-wip | Quantify abundances of transcripts from RNA-Seq data |
| wip/libGenome | 0.5.2 | pkgsrc-wip | Development library for bioinformatic software |
| wip/libghemical | 2.99.1 | pkgsrc-wip | Molecular modelling library |
| wip/libncl | 2.1.18 | pkgsrc-wip | The NEXUS Class Library is a C++ library for parsing NEXUS files |
| wip/liboglappth | 0.98 | pkgsrc-wip | Support libraries of science/ghemical port |
| wip/linux-ukbgene | ukbgene | pkgsrc-wip | Tool for accessing UK Biobank data |
| wip/maker | 3.01.04 | pkgsrc-wip | Genome annotation pipeline |
| wip/manatee | 1.8.4.1nb3 | pkgsrc-wip | Web-based gene evaluation and genome annotation tool |
| wip/metal | 2011.03.25 | pkgsrc-wip | Meta-analysis of genomewide association scans |
| wip/microbiomeutil | r20110519 | pkgsrc-wip | Utilities for processing and analyzing 16S rRNA genes |
| wip/microsynteny-tools | 0.1.0.175 | pkgsrc-wip | Tools for exploring microsyntenic differences among species |
| wip/minimap2 | 2.30 | pkgsrc-wip | Sequence alignment program for noisy, long reads |
| wip/mmdb | 1.25.6.1 | pkgsrc-wip | Macromolecular coordinate library |
| wip/mopac | 22.0.6 | pkgsrc-wip | Semi-empirical (MNDO, etc.) molecular orbital calculation |
| wip/mopac7 | 1.11 | pkgsrc-wip | Semi-empirical Quantum Chemistry Library |
| wip/mummer4 | 4.0.0.20201002 | pkgsrc-wip | Versatile alignment tool for DNA and protein sequences |
| wip/muscle | 3.8.31 | pkgsrc-wip | MUltiple Sequence Comparison by Log-Expectation |
| wip/nanoQC | 0.9.4.20200617 | pkgsrc-wip | Create fastQC-like plots for Oxford Nanopore sequencing data |
| wip/nanocomp | 1.15.0.20210602 | pkgsrc-wip | Compare runs of Oxford Nanopore sequencing data and alignments |
| wip/nanofilt | 2.8.0.20210223 | pkgsrc-wip | Filtering and trimming of Oxford Nanopore sequencing data |
| wip/nanoget | 1.16.1.20210320 | pkgsrc-wip | Extract information from Oxford Nanopore sequencing data |
| wip/nanolyse | 1.2.0.20200915 | pkgsrc-wip | Removing reads mapping to the lambda genome |
| wip/nanomath | 1.2.1.20210604 | pkgsrc-wip | Math functions for other Oxford Nanopore processing scripts |
| wip/nanopack | 0.0.0.20210524 | pkgsrc-wip | Long read processing and analysis scripts |
| wip/nanoplot | 1.38.0.20210602 | pkgsrc-wip | Plotting suite for Oxford Nanopore sequencing data and alignments |
| wip/nanostat | 1.5.0.20210108 | pkgsrc-wip | Statistics for Oxford Nanopore sequencing data and alignments |
| wip/ncbi | 20120620 | pkgsrc-wip | Portable, modular software for molecular biology |
| wip/ncbi-bin | 20120620 | pkgsrc-wip | Portable modular software for molecular biology |
| wip/ncbi-blast+ | src | pkgsrc-wip | NCBI implementation of Basic Local Alignment Search Tool |
| wip/ncbi-c++-lib | 20041130nb2 | pkgsrc-wip | Libraries needed by apps dependent on NCBI C++ toolkit |
| wip/ncbi-lib | 20120620 | pkgsrc-wip | Portable, modular software for molecular biology |
| wip/necat | pkgsrc-wip | Error correction and de-novo assembler Nanopore reads | |
| wip/p5-transdecoder | 5.3.0 | pkgsrc-wip | Identify candidate coding regions within transcript sequences |
| wip/p5-trimgalore | 0.4.4 | pkgsrc-wip | Wrapper around Cutadapt and FastQC for adapter and quality trimming |
| wip/peak-classifier | 0.1.4.21 | pkgsrc-wip | Classify ChIP/ATAC-Seq peaks based on features provided in a GFF |
| wip/pear | 0.9.6 | pkgsrc-wip | Memory-efficient and highly accurate pair-end read merger |
| wip/pear-merger | 0.9.6 | pkgsrc-wip | Memory-efficient and highly accurate pair-end read merger |
| wip/plink | 1.9b6.17 | pkgsrc-wip | Whole genome association analysis toolset |
| wip/plink2 | 0.0.0.20190202nb1 | pkgsrc-wip | Whole genome association analysis toolset |
| wip/pooler | 1.75 | pkgsrc-wip | Optimise DNA sequencing primer-set combinations |
| wip/preseq | 3.2.0 | pkgsrc-wip | Predict yield of distinct reads from a genomic library |
| wip/probcons | 1.12 | pkgsrc-wip | Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences |
| wip/prodigal | 2.6.3 | pkgsrc-wip | Prokaryotic Dynamic Programming Genefinding Algorithm |
| wip/py-achemkit | 0.3.0 | pkgsrc-wip | Artificial Chemistry Tookit |
| wip/py-ase | 3.8.1.3440nb2 | pkgsrc-wip | Atomic Simulation Environment |
| wip/py-bctpy | 0.3 | pkgsrc-wip | Brain Connectivity Toolbox for Python |
| wip/py-biofrills | 0.3.1 | pkgsrc-wip | Bioinformatics utilities for molecular sequence analysis |
| wip/py-cantera | pkgsrc-wip | Chemical kinetics, thermodynamics, and transport tool suite | |
| wip/py-cclib | 1.3nb1 | pkgsrc-wip | Parsers and algorithms for computational chemistry |
| wip/py-chemicals | 1.2.0 | pkgsrc-wip | Chemical properties component of ChEDL library |
| wip/py-chemlab | 0.3 | pkgsrc-wip | The python chemistry library you were waiting for |
| wip/py-chempy | 0.9.0 | pkgsrc-wip | Python package useful for solving problems in chemistry |
| wip/py-chemview | 0.1.1 | pkgsrc-wip | Interactive molecular viewer for IPython notebook |
| wip/py-cinfony | 1.0 | pkgsrc-wip | Common API for several cheminformatics toolkits |
| wip/py-cobra | 0.4.0b1 | pkgsrc-wip | Constraints-based modeling of biological networks |
| wip/py-cobrapy | 0.18.1 | pkgsrc-wip | Package for constraints-based modeling of biological networks |
| wip/py-cogent | 1.4.1 | pkgsrc-wip | Cogent A toolkit for statistical analysis of biological sequences |
| wip/py-csb | 1.2.3 | pkgsrc-wip | Computational Structural Biology Toolbox |
| wip/py-cutadapt | 5.2 | pkgsrc-wip | Find and remove adapter sequences, primers, poly-A tails, etc |
| wip/py-deap | 1.3.1 | pkgsrc-wip | Distributed Evolutionary Algorithms in Python |
| wip/py-diffpy-structure | 20090410 | pkgsrc-wip | Crystal structure container and parsers for structure formats |
| wip/py-dna-features-viewer | 3.1.3 | pkgsrc-wip | Python library to visualize DNA features, e.g. GenBank or Gff files |
| wip/py-dnaio | 1.2.0 | pkgsrc-wip | Read and write FASTQ and FASTA files |
| wip/py-eemeter | 0.5.3 | pkgsrc-wip | Open Energy Efficiency Meter |
| wip/py-epigrass | 2.3.1 | pkgsrc-wip | Epidemiological Geo-Referenced Analysis and Simulation System |
| wip/py-escher | 1.1.2.post2 | pkgsrc-wip | Build, view, share, and embed pathway maps |
| wip/py-ete3 | 3.1.1 | pkgsrc-wip | Python Environment for (phylogenetic) Tree Exploration |
| wip/py-fcsparser | 0.1.2 | pkgsrc-wip | Python package for reading raw fcs files |
| wip/py-gauss | 0.5.1 | pkgsrc-wip | Python API for Analysis of Gaussian Quantum Chemical Compuations |
| wip/py-geppy | 0.1 | pkgsrc-wip | Package for gene expression programming in Python |
| wip/py-gnm | 0.1 | pkgsrc-wip | Python Gaussian Network Model |
| wip/py-gpaw | 0.9.0.8965nb1 | pkgsrc-wip | Grid-based real-space PAW method DFT code |
| wip/py-htseq | 2.0.3 | pkgsrc-wip | Python library to facilitate programmatic analysis of sequence data |
| wip/py-inspyred | 1.0.1 | pkgsrc-wip | Bio-inspired computational intelligence algorithms in Python |
| wip/py-mappy | 2.18 | pkgsrc-wip | Minimap2 python binding |
| wip/py-mdanalysis | 0.15.0 | pkgsrc-wip | Library to analyze and manipulate molecular dynamics trajectories |
| wip/py-mdtraj | 1.8.0 | pkgsrc-wip | The analysis of molecular dynamics trajectories |
| wip/py-mendeleev | 0.1.0 | pkgsrc-wip | Database of atomic properties for elements in the periodic table |
| wip/py-mmLib | 1.2.0 | pkgsrc-wip | Python Macromolecular Library |
| wip/py-mne | 0.7.1 | pkgsrc-wip | MNE python project for MEG and EEG data analysis |
| wip/py-mol | 2.5.0 | pkgsrc-wip | Molecular Visualization System |
| wip/py-multiqc | 1.28 | pkgsrc-wip | Aggregate bioinformatics analysis reports across samples and tools |
| wip/py-neo | 0.3.3 | pkgsrc-wip | Python package for representing electrophysiology data |
| wip/py-nibabel | 1.3.0 | pkgsrc-wip | Access a multitude of neuroimaging data formats |
| wip/py-nilearn | 0.1.4.post1 | pkgsrc-wip | Statistical learning for neuroimaging in Python |
| wip/py-nipy | 0.3.0 | pkgsrc-wip | Python package for analysis of neuroimaging data |
| wip/py-nipy-data | 0.2 | pkgsrc-wip | Installation script for nipy data packages |
| wip/py-oasa | 0.13.1 | pkgsrc-wip | Python library for manipulation of chemical formats |
| wip/py-parameters | 0.2.1 | pkgsrc-wip | Hierarchical parameter sets for modelling and simulation |
| wip/py-periodictable | 1.4.1 | pkgsrc-wip | Extensible periodic table of the elements |
| wip/py-prody | 1.4.10 | pkgsrc-wip | Python Package for Protein Dynamics Analysis |
| wip/py-psychopy | 1.61.01nb4 | pkgsrc-wip | Psychology and neuroscience software in python |
| wip/py-pybigwig | 0.3.22 | pkgsrc-wip | Python access to bigWig files using libBigWig |
| wip/py-pydeseq2 | 0.5.2 | pkgsrc-wip | Python implementation of the popular DESeq2 R package |
| wip/py-pyevolve | 0.6rc1 | pkgsrc-wip | Complete genetic algorithm framework written in pure python |
| wip/py-pygr | 0.8.0nb1 | pkgsrc-wip | Pygr graph database for bioinformatics |
| wip/py-pymatgen | 2020.9.14 | pkgsrc-wip | Genomics is a robust materials analysis for structures and molecules |
| wip/py-pymvpa | pkgsrc-wip | Multivariate pattern analysis | |
| wip/py-pynn | 0.9.2 | pkgsrc-wip | Python package for neuronal network models |
| wip/py-pyquante | 1.6.3 | pkgsrc-wip | Quantum chemistry in Python |
| wip/py-pysam | 0.21.0 | pkgsrc-wip | Python module for reading, manipulating and writing genomic data sets |
| wip/py-pysb | 0.1.11 | pkgsrc-wip | Python Systems Biology modeling framework |
| wip/py-sima | 0.3.2 | pkgsrc-wip | Software for analysis of sequential imaging data |
| wip/py-spglib | 1.16.0 | pkgsrc-wip | Python bindings for finding and handling crystal symmetries |
| wip/py-sumatra | 0.5.2nb1 | pkgsrc-wip | Tracking projects based on numerical simulation or analysis |
| wip/py-thermo | 0.3.0 | pkgsrc-wip | Chemical properties component of ChEDL |
| wip/py-thermopy | 0.3 | pkgsrc-wip | Some utilities for Thermodynamics and Thermochemistry |
| wip/py-thermostat | 1.1.1 | pkgsrc-wip | Calculate connected thermostat savings |
| wip/py-tracks | pkgsrc-wip | Analysis tools for Molecular Dynamics and Monte Carlo simulations | |
| wip/py-varify | 0.7.0 | pkgsrc-wip | Clinical DNA Sequencing Analysis and Data Discovery |
| wip/r8s | 1.70 | pkgsrc-wip | Estimate rates of molecular evolution |
| wip/rainbow | 2.0.4 | pkgsrc-wip | Short reads clustering and local assembly |
| wip/raster3d | nb1 | pkgsrc-wip | Set of tools for generating raster images of proteins and molecules |
| wip/readseq | 2.1.19 | pkgsrc-wip | Read and reformat biosequences, Java command-line version |
| wip/repeatmasker | 4.1.2.1 | pkgsrc-wip | Find interspersed repeats and low complexity DNA sequences |
| wip/rna-seq | 1.3.0 | pkgsrc-wip | Core tools needed for RNA-Seq analysis |
| wip/rna-star | 2.7.11b | pkgsrc-wip | Spliced Transcripts Alignment to a Reference |
| wip/rsem | 1.2.30 | pkgsrc-wip | RNA-Seq by Expectation-Maximization |
| wip/salmon | 0.11.3 | pkgsrc-wip | Transcript-level quantification of RNA-seq from lightweight alignments |
| wip/samtools | 1.22 | pkgsrc-wip | Tools for manipulating sequence alignment maps |
| wip/scythe | 2016.02.10 | pkgsrc-wip | 3'-end adapter contaminant trimmer |
| wip/seqtk | 1.4 | pkgsrc-wip | Tool for processing sequences in FASTA/FASTQ format |
| wip/sickle | 1.33 | pkgsrc-wip | Windowed adaptive trimming tool for FASTQ files using quality |
| wip/slclust | 0.0.0.20100202 | pkgsrc-wip | Single-linkage clustering with Jaccard similarity |
| wip/smithwaterman | 0.0.0.20160702 | pkgsrc-wip | Smith-waterman-gotoh alignment algorithm |
| wip/spatt | pre7 | pkgsrc-wip | Statistics for Patterns |
| wip/sra-tools | 3.2.1nb1 | pkgsrc-wip | NCBI's toolkit for handling data in INSDC Sequence Read Archives |
| wip/stacks | 2.69 | pkgsrc-wip | Software pipeline for building loci from short-read sequences |
| wip/stringtie | 2.1.1 | pkgsrc-wip | Transcript assembly and quantification for RNA-seq |
| wip/structure | 2.3.4 | pkgsrc-wip | Multi-locus genotype data to investigate population structure |
| wip/subread | 2.1.0 | pkgsrc-wip | High-performance read alignment, quantification and mutation discovery |
| wip/t-coffee | 1.37 | pkgsrc-wip | Multiple Sequence Alignment Package |
| wip/tabixpp | 1.0.0.20171116 | pkgsrc-wip | C++ wrapper to tabix indexer |
| wip/tops-bin | 20030827 | pkgsrc-wip | Protein Topology Cartoons Tools |
| wip/treetool | 2.0.2 | pkgsrc-wip | Treetool is for displaying, editing, and printing phylogenetic trees |
| wip/trf | pkgsrc-wip | Genome tandom repeats finder | |
| wip/trimadap | 0.1.4 | pkgsrc-wip | Trim adapter sequences from Illumina data using heuristic rules |
| wip/trinity | 2.8.3 | pkgsrc-wip | Assembles transcript sequences from Illumina RNA-Seq data |
| wip/uchime | 4.2.40 | pkgsrc-wip | Algorithm for detecting chimeric sequences |
| wip/vcf-split | 0.1.5.19 | pkgsrc-wip | Split a multi-sample VCF into single-sample VCFs |
| wip/vcf2hap | 0.1.6.14 | pkgsrc-wip | Generate .hap file from VCF for haplohseq |
| wip/vcftools | 0.1.16 | pkgsrc-wip | Tools for working with VCF genomics files |
| wip/vsearch | 2.30.0 | pkgsrc-wip | Versatile open-source tool for metagenomics |
| wip/wise2 | 2.2.0nb1 | pkgsrc-wip | Tool for Comparing bio polymers like DNA and Protein sequences |
| wip/wise3 | 3 | pkgsrc-wip | TODO: Short description of the package |
| wip/xmatchview | pkgsrc-wip | Genome alignment visualization | |
| wip/xssp | 3.0.1 | pkgsrc-wip | Software for creating DSSP and HSSP files |