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

:: 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.

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.

PrIME 1.0.5 – Library and Accompanying tools for Phylogenetics

PrIME 1.0.5

:: DESCRIPTION

PrIME (Probabilistic Integrated Models of Evolution) is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling.

::DEVELOPER

PrIME  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PrIME

:: MORE INFORMATION

Citation:

Integrating Sequence Evolution into Probabilistic Orthology Analysis.
Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.
Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044

OBITools 1.2.13 – Scripts and Library for Sequence Analysis

OBITools 1.2.13

:: DESCRIPTION

OBITools is a set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.

::DEVELOPER

OBITools team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

 OBITools

:: MORE INFORMATION

Citation

OBITools: a Unix-inspired software package for DNA metabarcoding.
Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E.
Mol Ecol Resour. 2015 May 9. doi: 10.1111/1755-0998.12428.

Selene 0.4.8 – Library for deep-learning-based Sequence models

Selene 0.4.8

:: DESCRIPTION

Selene is a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Selene

:: MORE INFORMATION

Citation

Chen KM, Cofer EM, Zhou J, Troyanskaya OG.
Selene: a PyTorch-based deep learning library for sequence data.
Nat Methods. 2019 Apr;16(4):315-318. doi: 10.1038/s41592-019-0360-8. Epub 2019 Mar 28. PMID: 30923381; PMCID: PMC7148117.