FormalGrammars alternatives and similar packages

Based on the "Bioinformatics" category.
Alternatively, view FormalGrammars alternatives based on common mentions on social networks and blogs.

hemokit

8.4 0.0 FormalGrammars VS hemokit

Haskell library for the Emotiv EEG, inspired by the Emokit code
cobot

7.7 1.8 FormalGrammars VS cobot

Computational biology toolkit to collaborate with researchers in constructive protein engineering

InfluxDB – Built for High-Performance Time Series Workloads

InfluxDB 3 OSS is now GA. Transform, enrich, and act on time series data directly in the database. Automate critical tasks and eliminate the need to move data externally. Download now.

Promo www.influxdata.com

cobot-io

7.3 3.2 FormalGrammars VS cobot-io

Biological data file formats and IO
hPDB

7.2 0.0 FormalGrammars VS hPDB

PDB parser in Haskell
samtools

6.8 0.0 FormalGrammars VS samtools

DISCONTINUED. [Moved to: https://github.com/ingolia/SamTools]
RNAlien

6.5 0.0 FormalGrammars VS RNAlien

RNAlien - unsupervised RNA family model construction
phybin

6.2 0.0 FormalGrammars VS phybin

Binning (Newick) Phylogenetic Trees by Topology
bioinformatics-toolkit

5.5 0.0 FormalGrammars VS bioinformatics-toolkit

A collection of bioinformatics algorithms
Genbank

5.4 0.0 FormalGrammars VS Genbank

Genbank format tools and parser
BlastHTTP

5.1 0.0 FormalGrammars VS BlastHTTP

Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice
cobot-tools

5.0 3.6 FormalGrammars VS cobot-tools

DISCONTINUED. Biological data file formats and IO
vcf

5.0 0.0 FormalGrammars VS vcf

Haskell library to handle VCF (Variant Call Format) files
EntrezHTTP

4.8 0.0 FormalGrammars VS EntrezHTTP

Haskell cabal libary for submission and result retrieval from the NCBI Entrez REST webservice
cmv

4.8 0.0 FormalGrammars VS cmv

Visualize HMMs, CMs and their comparisons
TaxonomyTools

3.9 0.0 FormalGrammars VS TaxonomyTools

Tools to process and visualize NCBI taxonomy data
SelectSequencesFromMSA

3.9 0.0 FormalGrammars VS SelectSequencesFromMSA

Tool to select representative sequences from a multiple sequence alignment
Taxonomy

3.6 0.0 FormalGrammars VS Taxonomy

Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources.
ClustalParser

3.2 0.0 FormalGrammars VS ClustalParser

Parse output of Clustal tools
ViennaRNAParser

3.1 0.0 FormalGrammars VS ViennaRNAParser

Libary for parsing ViennaRNA package output
StockholmAlignment

2.9 0.0 FormalGrammars VS StockholmAlignment

Libary containing parsing and visualisation functions and datastructures for Stockholm aligmnent format.
memexml

2.8 0.0 FormalGrammars VS memexml

Haskell cabal libary for parsing Meme motif finder xml output
BioHMM

2.8 0.0 FormalGrammars VS BioHMM

Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format.
Forestry

1.9 0.0 FormalGrammars VS Forestry

Science and craft of forests
ADPfusionForest

1.7 0.0 FormalGrammars VS ADPfusionForest

Dynamic programming on tree and forest structures
Gene-CluEDO

1.6 0.0 FormalGrammars VS Gene-CluEDO

Gene Cluster Evolution Determined Order
MutationOrder

1.3 0.0 FormalGrammars VS MutationOrder

most likely order of mutation events in RNA
rank-product

1.2 0.0 FormalGrammars VS rank-product

Collects the functions pertaining to finding the rank product of a data set as well as the associated p-value.
seqloc

1.2 0.0 FormalGrammars VS seqloc

Bio.SeqLoc
uniprot-kb

1.1 0.0 FormalGrammars VS uniprot-kb

UniProt-KB format parser
mmtf

0.7 0.0 FormalGrammars VS mmtf

MMTF for Haskell
bio-sequence

- - FormalGrammars VS bio-sequence

DISCONTINUED. Initial project template from stack

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Popular Comparisons

README

FormalGrammars: A DSL for formal languages in Haskell

generalized Algebraic Dynamic Programming Homepage

The gADP homepage has a tutorial and example on how to write algorithms / grammars.

Ideas implemented here are described in a couple of papers:

Christian Hoener zu Siederdissen
Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming
2012, Proceedings of the 17th ACM SIGPLAN international conference on Functional programming
paper preprint
Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.
The HERMIT in the stream: fusing stream fusion’s concatMap
2014, Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.
paper
Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
Product Grammars for Alignment and Folding
2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99
paper
Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler
Algebraic Dynamic Programming over General Data Structures
2015, BMC Bioinformatics
preprint
Maik Riechert, Christian Höner zu Siederdissen, and Peter F. Stadler
Algebraic dynamic programming for multiple context-free languages
2016, Theoretical Computer Science
preprint