Tag: Library

BEETL 1.1.0 – Burrows-Wheeler Extended Tool Library

BEETL 1.1

:: DESCRIPTION

BEETL is a suite of applications for building and manipulating the Burrows-Wheeler Transform (BWT) of collections of DNA sequences. The algorithms employed in BEETL are intended to scale to collections of sequences containing one billion entries or more.

::DEVELOPER

BEETL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BEETL

:: MORE INFORMATION

Citation

BEETL-fastq: a searchable compressed archive for DNA reads.
Janin L, Schulz-Trieglaff O, Cox AJ.
Bioinformatics. 2014 Jun 20. pii: btu387.

BMC Bioinformatics. 2013;14 Suppl 5:S2. doi: 10.1186/1471-2105-14-S5-S2. Epub 2013 Apr 10.
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
Ander C1, Schulz-Trieglaff OB, Stoye J, Cox AJ.

GeLL 2.0 – General Likelihood Library for use in Phylogenetics

GeLL 2.0

:: DESCRIPTION

GeLL is a General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques.

::DEVELOPER

Daniel Money

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 GeLL

:: MORE INFORMATION

Citation

GeLL: A Generalized Likelihood Library for Phylogenetic Models.
Money D, Whelan S.
Bioinformatics. 2015 Feb 27. pii: btv126.

TRAL 2.0 – Tandem Repeat Annotation Library

TRAL 2.0

:: DESCRIPTION

TRAL makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.

::DEVELOPER

TRAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  TRAL

:: MORE INFORMATION

Citation

TRAL: Tandem repeat annotation library.
Schaper E, Korsunsky A, Messina A, Murri R, Pečerska J, Stockinger H, Zoller S, Xenarios I, Anisimova M.
Bioinformatics. 2015 May 18. pii: btv306.

e!DAL 3.0.4 – Electronic Data Archive Library

e!DAL 3.0.4

:: DESCRIPTION

e!DAL is a lightweight open source software software framework for publishing and sharing research data.

::DEVELOPER

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

:: SCREENSHOTS

eDAL

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 e!DAL

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Jun 24;15:214. doi: 10.1186/1471-2105-15-214.
e!DAL–a framework to store, share and publish research data.
Arend D1, Lange M, Chen J, Colmsee C, Flemming S, Hecht D, Scholz U.

tqDist 1.0.2 – a Triplet and Quartet Distance Library

tqDist 1.0.2

:: DESCRIPTION

tqDist is a software package for computing the triplet and quartet distances between general rooted or unrooted trees, respectively.

::DEVELOPER

Christian N. S. Pedersen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R / Python

:: DOWNLOAD

  tqDist

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 10. [Epub ahead of print]
tqDist: a library for computing the quartet and triplet distances between binary or general trees.
Sand A1, Holt MK, Johansen J, Brodal GS, Mailund T, Pedersen CN.

zipHMM 1.0.1 – Library for very fast Likelihood Computations for Hidden Markov Models

zipHMM 1.0.1

:: DESCRIPTION

zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.

::DEVELOPER

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 zipHMM

:: MORE INFORMATION

Citation:

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A, Kristiansen M, Pedersen CN, Mailund T.
BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.

Brain 1.5.1 – Library for Biomedical Knowledge Manipulation

Brain 1.5.1

:: DESCRIPTION

Brain helps you to quickly and easily buid OWL ontologies and knowledge bases.

::DEVELOPER

Samuel Croset

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Brain

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1238-9. doi: 10.1093/bioinformatics/btt109. Epub 2013 Mar 16.
Brain: biomedical knowledge manipulation.
Croset S1, Overington JP, Rebholz-Schuhmann D.

ms-data-core-api 2.0.5 – Metadata-oriented Library for Computational Proteomics

ms-data-core-api 2.0.5

:: DESCRIPTION

The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines.

::DEVELOPER

ms-data-core-api team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PRIDE

:: DOWNLOAD

 ms-data-core-api

:: MORE INFORMATION

Citation

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.
Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250.

ImgLib2 2-5.12.0 – Image Processing JAVA Library

ImgLib2 2-5.12.0

:: DESCRIPTION

ImgLib2 is a general-purpose, multidimensional image processing library.

::DEVELOPER

ImgLib2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  ImgLib2

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):3009-11. doi: 10.1093/bioinformatics/bts543. Epub 2012 Sep 8.
ImgLib2–generic image processing in Java.
Pietzsch T, Preibisch S, Tomancák P, Saalfeld S.

DART – Library includes a number of Bioinformatics Alignment Programs

DART

:: DESCRIPTION

The DART (DNA, Amino and RNA Tests.)library includes a number of bioinformatics programs, including: stemloc for RNA alignment; xrate for phylo-grammars; phylocomposer and other statistical alignment programs in the Handel package; and more.The programs use statistical algorithms (MCMC, EM) to impute multiple alignments, annotations and other unseen evolutionary parameters from sequence data. All are based on stochastic grammars or state-machine models of sequence mutation and natural selection.

::DEVELOPER

Ian Holmes, Berkeley

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DART

:: MORE INFORMATION

Citation:

Paper Archive.