Tag: Bioinformatics

Bioconductor 3.13 – Open Source Software for Bioinformatics

Bioconductor 3.13

:: DESCRIPTION

Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

::DEVELOPER

Bioconductor Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Bioconductor

:: MORE INFORMATION

Publications

Geneious 2021.1 – Bioinformatics Software Suite

Geneious 2021.1

:: DESCRIPTION

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and cloning, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more.

::DEVELOPER

Biomatters Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Geneious

:: MORE INFORMATION

Citation

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A.
Bioinformatics. 2012 Jun 15;28(12):1647-9.

QIAGEN CLC Main Workbench 21.0.4 – Bioinformatics Workbench

QIAGEN CLC Main Workbench 21.0.4

:: DESCRIPTION

QIAGEN CLC Main Workbench is a bioinformatics workbench.CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

::DEVELOPER

QIAGEN

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window

:: DOWNLOAD

CLC Main Workbench

:: MORE INFORMATION

MolQuest 2.4.5 – Bioinformatics Toolbox for Analysis of Biomedical Data

MolQuest 2.4.5

:: DESCRIPTION

MolQuest is the most comprehensive, easy-to-use desktop application for sequence analysis and molecular biology data management.Each package provides an user-friendly interface for primer design, internet database searches, gene prediction, promoter identification, regulatory elements mapping, patterns discovery protein analysis, multiple sequences alignment, phylogenetic reconstruction, and a wide variety of other functions.

::DEVELOPER

Softberry, Inc

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MolQuest

:: MORE INFORMATION

Bpipe 0.9.10 – A Tool for Running and Managing Bioinformatics Pipelines

Bpipe 0.9.10

:: DESCRIPTION

Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages – known as ‘pipelines’.

::DEVELOPER

Bpipe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Bpipe

:: MORE INFORMATION

Citation:

Bpipe: a tool for running and managing bioinformatics pipelines.
Sadedin SP, Pope B, Oshlack A.
Bioinformatics. 2012 Jun 1;28(11):1525-6. doi: 10.1093/bioinformatics/bts167.

MoSDi 1.3 – Sequence Analysis Toolkit for Bioinformatics

MoSDi 1.3

:: DESCRIPTION

MoSDi (Motif Statistics and Discovery) contains a lot of sequence analysis algorithms, including methods for

  • motif statistics, e.g. compute the exact occurrence count distribution of a motif,
  • exact motif discovery: extraction of motifs with provably optimal p-value,
  • analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text,
  • statistics of fragment masses resulting from proteolytic cleavage of proteins,
  • computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent),
  • analysing sensitivity of spaced alignment seeds.

::DEVELOPER

Tobias Marschall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java 

:: DOWNLOAD

 MoSDi

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1737-50.
Probabilistic arithmetic automata and their applications.
Marschall T, Herms I, Kaltenbach HM, Rahmann S.

BATMat – Bioinformatics Autodiscovery of Training Materials

BATMat

:: DESCRIPTION

BATMat is a Google-based, open source, automatic search tool for training materials.

::DEVELOPER

Billy Lapatas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BATMat

:: MORE INFORMATION

Citation:

BATMat: Bioinformatics Autodiscovery of Training Materials.
Lapatas V, Stefanidakis M.
Brief Bioinform. 2015 Sep 1. pii: bbv071.

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