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wip/ufc Unified framework for finite element assembly
wip/py-sparqlwrapper SPARQL endpoint interface to Python
wip/py-instant Instant inlining of C and C++ code in Python
wip/pbseqan PacBio patched and stripped down seqan
wip/cereal C++11 library for serialization
wip/tbb Library that provides thread building blocks
wip/salmon Transcript-level quantification of RNA-seq from lightweight alignments
wip/cdhit Clustering and comparing protein or nucleotide sequences
wip/jellyfish Fast, memory-efficient counting of k-mers in DNA
wip/vcflib C++ library and CLI tools for parsing and manipulating VCF files
biology/trimmomatic Flexible read trimming tool for Illumina NGS data
wip/gtextutils Gordon text utilities
wip/yaggo Generate command line parser using getopt_long
wip/ganglia-webfrontend PHP based frontend for the Ganglia Cluster Monitor
wip/numactl Non Uniform Memory Access tools
wip/slurm Simple Linux Utility for Resource Management
wip/daligner Find all significant local alignments between reads
wip/bpcscripts Gast Illumina processing
wip/webbrowser TODO: Short description of the package
wip/meep-openmpi FDTD simulation software to model electromagnetic systems
wip/parafly Process the commands in parallel on a single server
wip/dlpoly-classic General purpose classical molecular dynamics
wip/py-ffc C++ code generator for multilinear forms
wip/R-mpfr Multiple Precision Floating Point Arithmetic for R
wip/pear Memory-efficient and highly accurate pair-end read merger
wip/py-ufl Unified Form Language for finite element discretizations
wip/suitesparse SuiteSparse is a set of packages for sparse matrices calculation
wip/pbbam PacBio BAM C++ library, with SWIG bindings
wip/plink Whole genome association analysis toolset
wip/cblas C bindings and headers for BLAS library
wip/metal Meta-analysis of genomewide association scans
wip/structure Multi-locus genotype data to investigate population structure
wip/R-cellranger Helper functions to work with spreadsheets
wip/seqtk Tool for processing sequences in FASTA/FASTQ format
wip/lmod Dynamic modification of a users environment
wip/jellyfish2 Fast, memory-efficient counting of k-mers in DNA
wip/cufflinks-2.2.1 RNA transcript assembly, differential expression/regulation
wip/fftw-mpich Collection of fast C routines to compute DFTs
wip/fastool Simple and quick FastQ and FastA tool for file reading and conversion
wip/R-readxl Import excel files into R
wip/mpb MIT Photonic Bands
wip/ddocent Bash pipeline for RAD sequencing
wip/armadillo C++ linear algebra library
wip/pbcopper Core C++ library for data structures, algorithms, and utilities
wip/epacts Efficient and Parallelizable Association Container Toolbox
wip/py-fiat Finite element Automatic Tabulator
wip/antlr ANother Tool for Language Recognition
wip/rainbow Short reads clustering and local assembly
wip/unanimity Consensus library and applications
wip/rsem RNA-Seq by Expectation-Maximization
wip/bolt-lmm Statistics for testing association between phenotype and genotypes
wip/meep-mpi FDTD simulation software to model electromagnetic systems
wip/cdbfasta Fast indexing and retrieval of fasta records from flat file databases
wip/samtools Tools for manipulating next-generation sequencing data
wip/munge Authentication service for creating and validating credentials
wip/man2html Convert nroff(1) man pages to HTML
wip/py-pypeflow Lightweight and reusable make/flow data process library
wip/auto-admin Automate common systems administration tasks
wip/dolfin C++/Python interface of FEniCS
wip/fvcom2 Prognostic coastal ocean circulation model
wip/bowtie Ultrafast, memory-efficient short read aligner
wip/mpb-openmpi MIT Photonic Bands
wip/vcftools Tools for working with VCF genomics files
wip/py-rdflib340 Python library for RDF manipulation
wip/py-viper Scientific plotter and run-time visualization module
wip/py-macs2 Novel algorithm for identifying transcript factor binding sites
wip/p5-trimgalore Wrapper around Cutadapt and FastQC for adapter and quality trimming
wip/fbsd2pkg Convert a FreeBSD port framework to a pkgsrc package
biology/bwa Map low-divergent sequences against a large reference genome
wip/tabixpp C++ wrapper to tabix indexer
devel/py-xopen Open compressed files transparently
wip/fastqc Quality control tool for high throughput sequence data
wip/fastahack Utilities for indexing and sequence extraction from FASTA files
wip/py-hostlist Manage SLURM host lists
wip/fftw-openmpi Collection of fast C routines to compute DFTs
wip/bwa Map low-divergent sequences against a large reference genome
wip/openmx-openmpi Nano-scale material simulations based on DFT
wip/trimmomatic Flexible read trimming tool for Illumina NGS data
wip/denyhosts Block hosts with too many failed login attempts
wip/multichoose Generate multiset combinations (n multichoose k)
wip/dazz_db Dresden assembler for long read DNA projects
wip/filevercmp Filevercmp function as in sort --version-sort
wip/htslib C library for high-throughput sequencing data formats
parallel/ganglia-monitor-core Ganglia cluster monitor, monitoring daemon
wip/gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
wip/fastaunique Sort and uniq fasta files
wip/fsom Tiny C library for managing SOM (Self-Organizing Maps) neural networks
wip/slclust Single-linkage clustering with Jaccard similarity
wip/py-pbfalcon Experimental PacBio diploid assembler
wip/samtools0119 Generic format for storing large nucleotide sequence alignments
wip/py-cutadapt Finds and removes adapter sequences, primers, poly-A tails, etc
wip/p5-IPC-Open3-Simple Simple alternative to IPC::Open3
wip/smithwaterman Smith-waterman-gotoh alignment algorithm
wip/linux-ukbgene Tool for accessing UK Biobank data
wip/mcl Fast and scalable unsupervised cluster algorithm for graphs
wip/trinity Assembles transcript sequences from Illumina RNA-Seq data
wip/blasr_libcpp Library for analyzing PacBio sequences
wip/bedtools2 Swiss army knife for genome arithmetic
wip/p5-transdecoder Identify candidate coding regions within transcript sequences
wip/tophat Fast splice junction mapper for RNA-Seq reads
wip/py-rdfextras Collection of packages providing extras based on RDFLib 3
wip/meep FDTD simulation software to model electromagnetic systems
wip/blasr PacBio(R) long read aligner
wip/py-anvio Analysis and visualization platform for omics data
wip/libzeep Make it easy to create SOAP servers
wip/R-getopt C-Like getopt Behavior
wip/py-biopython Collection of Python modules for bioinformatics
wip/xssp Software for creating DSSP and HSSP files
wip/py-pysam Python module for reading, manipulating and writing genomic data sets
wip/R-optparse Command Line Option Parser
wip/famsa Algorithm for large-scale multiple sequence alignments
wip/py-ete3 Python Environment for (phylogenetic) Tree Exploration
wip/py-snakemake Reduce the complexity of creating workflows
wip/py-eggnog-mapper Fast functional annotation of novel DNA or protein sequences
wip/R-rematch Wrapper on regexpr to extract matches and captured groups
wip/pkg-dev Tools for pkgsrc development and testing
wip/fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
wip/hmmer Profile hidden Markov models for biological sequence analysis
wip/py-xopen Open compressed files transparently
wip/vsearch Versatile open-source tool for metagenomics
textproc/man2html Convert nroff(1) man pages to HTML
wip/py-htseq Framework to analyze data from high-throughput sequencing assays
wip/slurm-spank-x11 Enables to export X11 display on allocated nodes
wip/intervaltree Minimal C++ interval tree implementation
wip/kallisto Quantify abundances of transcripts from RNA-Seq data
wip/bowtie2 Ultrafast, memory-efficient short read aligner
wip/muscle MUltiple Sequence Comparison by Log-Expectation
wip/bcftools Tools for manipulating BCF (binary VCF) sequence files
wip/prodigal Prokaryotic Dynamic Programming Genefinding Algorithm
parallel/slurm-wlm Simple Linux Utility for Resource Management
wip/wgrib2 Tools for managing GRIB weather data files
biology/ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
biology/htslib C library for high-throughput sequencing data formats
wip/plink2 Whole genome association analysis toolset
biology/samtools Tools for manipulating next-generation sequencing data
wip/R-data.table Extension of data.frame
wip/canu Single molecule sequence assembler for genomes large and small
wip/singularity Application container for Linux
wip/centrifuge Novel microbial classification engine
security/munge Authentication service for creating and validating credentials