Bioinformatics

@hackage/ADPfusion

Efficient, high-level dynamic programming.

@hackage/ADPfusionForest

Dynamic programming on tree and forest structures

@hackage/ADPfusionSet

Dynamic programming for Set data structures.

@hackage/AlignmentAlgorithms

Collection of alignment algorithms

@hackage/BCMtools

Big Contact Map Tools

@hackage/BioHMM

Libary for Hidden Markov Models in HMMER3 format.

@hackage/Biobase

Base library for bioinformatics

@hackage/BiobaseBlast

BLAST-related tools

@hackage/BiobaseDotP

Vienna / DotBracket / ExtSS parsers

@hackage/BiobaseEnsembl

Ensembl related datastructures and functions

@hackage/BiobaseFR3D

Importer for FR3D resources

@hackage/BiobaseFasta

streaming FASTA parser

@hackage/BiobaseHTTP

Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl

@hackage/BiobaseHTTPTools

Tools to query Bioinformatics HTTP services e.g. Entrez, Ensembl.

@hackage/BiobaseInfernal

Infernal data structures and tools

@hackage/BiobaseMAF

Multiple Alignment Format

@hackage/BiobaseNewick

Newick file format parser.

@hackage/BiobaseTrainingData

RNA folding training data

@hackage/BiobaseTurner

Import Turner RNA parameters

@hackage/BiobaseTypes

Collection of types for bioinformatics

@hackage/BiobaseVienna

Import Vienna energy parameters

@hackage/BiobaseXNA

Efficient RNA/DNA/Protein Primary/Secondary Structure

@hackage/BlastHTTP

Libary to interface with the NCBI blast REST interface

@hackage/CMCompare

Infernal covariance model comparison

@hackage/ClustalParser

Libary for parsing Clustal tools output

@hackage/DnaProteinAlignment

Frameshift-aware alignment of protein sequences with DNA sequences

@hackage/EntrezHTTP

Libary to interface with the NCBI Entrez REST service.

@hackage/ForestStructures

Tree- and forest structures

@hackage/Forestry

Comparison of trees and forests.

@hackage/FormalGrammars

(Context-free) grammars in formal language theory

@hackage/Genbank

Libary for processing the NCBI genbank format

@hackage/Gene-CluEDO

Hox gene clustering

@hackage/GenussFold

MCFGs for Genus-1 RNA Pseudoknots

@hackage/GrammarProducts

Grammar products and higher-dimensional grammars

@hackage/MC-Fold-DP

Folding algorithm based on nucleotide cyclic motifs.

@hackage/MutationOrder

Most likely order of mutation events in RNA

@hackage/Nussinov78

Nussinov78 using the ADPfusion library.

@hackage/PDBtools

A library for analysis of 3-D protein coordinates

@hackage/RNAFold

RNA secondary structure prediction

@hackage/RNAFoldProgs

RNA secondary structure folding

@hackage/RNAdesign

Multi-target RNA sequence design

@hackage/RNAdraw

Draw RNA secondary structures

@hackage/RNAlien

Unsupervized construction of RNA family models

@hackage/RNAwolf

RNA folding with non-canonical basepairs and base-triplets.

@hackage/SelectSequencesFromMSA

Selects a representative subset of sequences from multiple sequence alignment.

@hackage/StockholmAlignment

Libary for Stockholm aligmnent format

@hackage/Taxonomy

Libary for parsing, processing and vizualization of taxonomy data

@hackage/TaxonomyTools

Tool for parsing, processing, comparing and visualizing taxonomy data

@hackage/ViennaRNA-bindings

ViennaRNA v2 bindings

@hackage/ViennaRNA-extras

ViennaRNA v2 extensions

@hackage/ViennaRNAParser

Libary for parsing ViennaRNA package output

@hackage/a50

Compare genome assemblies

@hackage/adp-multi

ADP for multiple context-free languages

@hackage/adp-multi-monadiccp

Subword construction in adp-multi using monadiccp

@hackage/bamstats

A program to extract various information from BAM alignmnet files.

@hackage/bio

A bioinformatics library

@hackage/bioace

Library for reading ace assembly files

@hackage/bioalign

Data structures and helper functions for calculating alignments

@hackage/biocore

A bioinformatics library

@hackage/biofasta

Library for reading fasta sequence files

@hackage/biofastq

A library for reading FASTQ files

@hackage/biohazard

bioinformatics support library

@hackage/biophd

Library for reading phd sequence files

@hackage/biopsl

Library and executables for working with PSL files

@hackage/biosff

Library and executables for working with SFF files

@hackage/biostockholm

Parsing and rendering of Stockholm files (used by Pfam, Rfam and Infernal).

@hackage/birch-beer

Plot a colorful tree.

@hackage/blastxml

Library for reading Blast XML output

@hackage/blosum

BLOSUM generator

@hackage/classify-frog

Classify sounds produced by Xenopus laevis

@hackage/clustertools

Tools for manipulating sequence clusters

@hackage/cmv

Detailed visualization of CMs, HMMs and their comparisions

@hackage/collapse-duplication

Collapse the duplication output into clones and return their frequencies.

@hackage/convert-annotation

Convert the annotation of a gene to another in a delimited file using a variety of different databases.

@hackage/dephd

Analyze quality of nucleotide sequences.

@hackage/differential

Finds out whether an entity comes from different distributions (statuses).

@hackage/diversity

Quantify the diversity of a population

@hackage/elynx

Validate and (optionally) redo ELynx analyses

@hackage/elynx-markov

Simulate molecular sequences along trees

@hackage/elynx-nexus

Import and export Nexus files

@hackage/elynx-seq

Handle molecular sequences

@hackage/elynx-tools

Tools for ELynx

@hackage/elynx-tree

Handle phylogenetic trees

@hackage/estreps

Repeats from ESTs

@hackage/flower

Analyze 454 flowgrams (.SFF files)

@hackage/flowsim

Simulate 454 pyrosequencing

@hackage/gact

General Alignment Clustering Tool

@hackage/hPDB

Protein Databank file format library

@hackage/hPDB-examples

Examples for hPDB library

@hackage/hTalos

Parser, print and manipulate structures in PDB file format.

@hackage/heatitup

Find and annotate ITDs.

@hackage/heatitup-complete

Find and annotate ITDs with assembly or read pair joining.

@hackage/hemokit

Haskell port of the Emokit EEG project

@hackage/hierarchical-spectral-clustering

Hierarchical spectral clustering of a graph.

@hackage/hs-samtools

Read and write SAM, BAM, and CRAM files.

@hackage/hyraxAbif

Modules for parsing, generating and manipulating AB1 files.

@hackage/integreat

Integrate different assays.

@hackage/korfu

The Korfu ORF Utility

@hackage/memexml

Library for reading Meme XML output

@hackage/mmtf

Macromolecular Transmission Format implementation

@hackage/modify-fasta

Modify fasta (and CLIP) files in several optional ways

@hackage/modularity

Find the modularity of a network.

@hackage/normalize

Normalize data using a variety of methods.

@hackage/phybin

Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance.

@hackage/pipes-ordered-zip

merge two ordered Producers into a new Producer

@hackage/ploterific

Basic plotting of tabular data for the command line.

@hackage/rank-product

Find the rank product of a data set.

@hackage/rbr

Mask nucleotide (EST) sequences in Fasta format

@hackage/samtools

Binding to the C samtools library

@hackage/samtools-conduit

Conduit interface to SAM/BAM format files through samtools

@hackage/samtools-enumerator

Enumerator interface to SamTools library

@hackage/samtools-iteratee

Iteratee interface to SamTools library

@hackage/seqloc

Handle sequence locations for bioinformatics

@hackage/seqloc-datafiles

Read and write BED and GTF format genome annotations

@hackage/sequence-formats

A package with basic parsing utilities for several Bioinformatic data formats.

@hackage/sequenceTools

A package with tools for processing DNA sequencing data

@hackage/sgrep

Sgrep - grep Fasta files for sequences matching a regular expression

@hackage/simseq

Simulate sequencing with different models for priming and errors

@hackage/slynx

Handle molecular sequences

@hackage/smiles

@hackage/subsample

Subsample data.

@hackage/tex-join-bib

Compile separate tex files with the same bibliography.

@hackage/tlynx

Handle phylogenetic trees

@hackage/too-many-cells

Cluster single cells and analyze cell clade relationships.

@hackage/trimpolya

Search for, annotate and trim poly-A tail

@hackage/twobitreader

reader for the 2bit file format

@hackage/varan

Process mpileup output to identify significant differences

@hackage/vcf

A package to parse VCF files inspired in similar python libraries

@hackage/xml2x

Convert BLAST output in XML format to CSV or HTML

@hackage/xsact

Cluster EST sequences

@hackage/zsyntax

Automated theorem prover for the Zsyntax biochemical calculus