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Category listing - biology (List all)
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Previous | Query returned 143 packages, results 1 to 100 | Next

ad2vcf		Add allelic depth info from a SAM stream to a VCF file
arka		Graphic interface for the programs from the GP package
atac-seq		Core tools needed for ATAC-Seq analysis
azara		Programs to process and view NMR data
balance-tui		Balance chemical equations from the CLI
bcf-score		Bcftools plugin for mosaic chromosomal alteration analysis
bcftools		Tools for manipulating BCF and VCF variant call files
beagle		Phasing genotypes and imputing ungenotyped markers
bedtools		Swiss army knife for genome arithmetic
bio-mocha		Bcftools plugin for mosaic chromosomal alteration analysis
biolibc		Low-level high-performance bioinformatics library
biolibc-tools		High-performance bioinformatics tools based on biolibc
bioperl		Perl tools for computational molecular biology
bioruby (V)		Intergrated environment for Bioinformatics using Ruby
biostar-tools (V)		Meta-package for Biostar Handbook tools
bodr		Blue Obelisk Data Repository
bowtie2		Ultrafast, memory-efficient short read aligner
bwa		Map low-divergent sequences against a large reference genome
canu		Single molecule sequence assembler for genomes large and small
cdhit		Clustering and comparing protein or nucleotide sequences
chemtool		Program for drawing organic molecules
chip-seq		Core tools needed for ChIP-Seq analysis
clustalw		General purpose multiple alignment program for DNA or proteins
coalesce		Estimates effective population size and mutation rate
coordgenlibs		2D coordinate generation for molecules
fasda		Fast and simple differential analysis
fastDNAml		Program derived from Joseph Felsenstein's version 3.3 DNAML
fastp		Ultra-fast all-in-one FASTQ preprocessor
fastq-trim		Lightening fast sequence read trimmer
fastqc		Quality control tool for high throughput sequence data
fasttree		Approximately-maximum-likelihood phylogenetic trees from alignments
fastx-toolkit		CLI tools for Short-Reads FASTA/FASTQ files preprocessing
filter-fastq		Filter reads from a FASTQ file
fluctuate		Estimation of population growth rate
gabedit		Graphical User Interface to computational chemistry packages
generand		Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
genesplicer		Computational Method for Splice Site Prediction
gffread		GFF/GTF format conversions, filtering, FASTA extraction, etc
glimmer		System for finding genes in microbial DNA
gp		Manipulate DNA/RNA sequence in a Unix fashion
gromacs		Molecular dynamics package
haplohseq		Identify regions of allelic imbalance
hisat2		Alignment program for mapping next-generation sequencing reads
hmmer		Implementation of profile HMM software for protein sequence analysis
htslib		C library for high-throughput sequencing data formats
igv		Visualization tool for genomic datasets
jmol (V)		Jmol: an open-source Java viewer for chemical structures in 3D
kallisto		Quantify abundances of transcripts from RNA-Seq data
libpll		High-performance software library for phylogenetic analysis
lucy		Sequence Cleanup Program
maeparser		Parser for Maestro file format
mca-calling		Core tools for Mosaic Chromosomal Alteration event calling
microsynteny-tools		Tools for exploring microsyntenic differences among species
miniasm		OLC-based de novo assembler for long reads
minimap2		Sequence alignment program for noisy, long reads
mmdb (V)		Macromolecular coordinate library
molsketch		Program for drawing molecular structures
mopac		Semi-empirical (MNDO, etc.) molecular orbital calculation
mpqc		The Massively Parallel Quantum Chemistry Program
mummer		System for aligning whole genome sequences
nanocomp (V)		Compare runs of Oxford Nanopore sequencing data and alignments
nanofilt (V)		Filtering and trimming of Oxford Nanopore sequencing data
nanoget (V)		Extract information from Oxford Nanopore sequencing data
nanolyse (V)		Removing reads mapping to the lambda genome
nanomath (V)		Math functions for other Oxford Nanopore processing scripts
nanoplot (V)		Plotting suite for Oxford Nanopore sequencing data and alignments
nanoQC (V)		Create fastQC-like plots for Oxford Nanopore sequencing data
nanostat (V)		Statistics for Oxford Nanopore sequencing data and alignments
ncbi-blast+		NCBI implementation of Basic Local Alignment Search Tool
nutsqlite		Record what you eat and analyze your meals
openbabel		Chemistry file translation program
p5-Bio-ASN1-EntrezGene		Regular expression-based Perl Parser for NCBI Entrez Gene
pdbalign		Prediction of Protein Secondary Structure and Active Sites
peak-classifier		Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
phylip		Phylogeny Inference Package
plink		Whole-genome association analysis toolset
plinkseq		C/C++ library for working with human genetic variation data
primer3		Design PCR primers
profit		Performs least squares fits of two protein structures
puzzle		Maximum likelihood analysis of molecular sequence data
py-ase (V)		Atomic Simulation Environment
py-bcbio-gff		Read and write Generic Feature Format (GFF) with Biopython integration
py-biofrills (V)		Bioinformatics utilities for molecular sequence analysis
py-biopython		Python libraries for computational molecular biology
py-cantera (V)		Chemical kinetics, thermodynamics, and transport tool suite
py-cclib (V)		Parsers and algorithms for computational chemistry
py-chemicals (V)		Chemical properties component of ChEDL library
py-chempy (V)		Python package useful for solving problems in chemistry
py-cobrapy (V)		Package for constraints-based modeling of biological networks
py-cogent (V)		Cogent A toolkit for statistical analysis of biological sequences
py-csb (V)		Computational Structural Biology Toolbox
py-cutadapt		Find and remove adapter sequences, primers, poly-A tails, etc
py-deap (V)		Distributed Evolutionary Algorithms in Python
py-dna-features-viewer		Python library to visualize DNA features, e.g. GenBank or Gff files
py-dnaio		Read and write FASTQ and FASTA files
py-geppy (V)		Package for gene expression programming in Python
py-gnm (V)		Python Gaussian Network Model
py-gpaw (V)		Grid-based real-space PAW method DFT code
py-htseq (V)		Python library to facilitate programmatic analysis of sequence data
py-macs2		Algorithm for identifying transcription factor binding sites

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