GENtle2 0.7.0 – Web-Based DNA Editor for Synthetic Biology

GENtle2 0.7.0

:: DESCRIPTION

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

::DEVELOPER

Synbiota Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

  GENtle

:: MORE INFORMATION

Biopieces 2.0 – Bioinformatic Framework of Tools

Biopieces 2.0

:: DESCRIPTION

The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.

::DEVELOPER

Martin Asser Hansen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Biopieces

:: MORE INFORMATION

Artemis v18.0.3 – Genome Browser and Annotation Tool

Artemis v18.0.3

:: DESCRIPTION

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

Artemis

:: MORE INFORMATION

Citation

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Artemis: sequence visualization and annotation.
Bioinformatics (Oxford, England) 2000;16;10;944-5

GenVisR 1.16.1 – Genome Data Visualizations

GenVisR 1.16.1

:: DESCRIPTION

Intuitively visualizing and interpreting data from high-throughput genomic technologies continues to be challenging.GenVisR (“Genomic Visualizations in R”) attempts to alleviate this burden by providing highly customizable publication-quality graphics supporting multiple species and focused primarily on a cohort level (i.e., multiple samples/patients). GenVisR attempts to maintain a high degree of flexibility while leveraging the abilities of ggplot2 and bioconductor to achieve this goal.

::DEVELOPER

The Griffith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R/ BioConductor

:: DOWNLOAD

 GenVisR

:: MORE INFORMATION

Citation

GenVisR: Genomic Visualizations in R.
Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M.
Bioinformatics. 2016 Jun 10. pii: btw325.

IGB 9.0.2 – Visualization for Genome-scale Data

IGB 9.0.2

:: DESCRIPTION

IGB (Integrated Genome Browser) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.

::DEVELOPER

IGB team Department of Bioinformatics and Genomics, University of North Carolina at Charlotte

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

IGB

:: MORE INFORMATION

Citation:

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Bioinformatics. 2009 Oct 15;25(20):2730-1.

caOmicsV 1.14.0 – Visualization of Multi-dimentional Cancer Genomics data

caOmicsV 1.14.0

:: DESCRIPTION

caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.

::DEVELOPER

Henry Zhang <hzhang at mail.nih.gov>

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R / BioConductor

:: DOWNLOAD

 caOmicsV

:: MORE INFORMATION

Citation

caOmicsV: an R package for visualizing multidimensional cancer genomic data.
Zhang H, Meltzer PS, Davis SR.
BMC Bioinformatics. 2016 Mar 22;17(1):141. doi: 10.1186/s12859-016-0989-6.

TASUKE ver.20190826 – Visualization program for Large-scale Resequencing data

TASUKE ver.20190826

:: DESCRIPTION

TASUKE is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies.The variation and read depth of multiple genomes, as well as annotations, can be shown simultaneously at various scales.

::DEVELOPER

Bioinformatics Research Unit, Agrogenomics Research Center

:: SCREENSHOTS

TASUKE

:: REQUIREMENTS

  • Linux
  • Apach
  • Php
  • MySQL

:: DOWNLOAD

 TASUKE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1806-8. doi: 10.1093/bioinformatics/btt295. Epub 2013 Jun 7.
TASUKE: a web-based visualization program for large-scale resequencing data.
Kumagai M1, Kim J, Itoh R, Itoh T.

Metaxa2 2.2 – Identification and Classification of Small Subunit (SSU) rRNA Sequences

Metaxa2 2.2

:: DESCRIPTION

Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

::DEVELOPER

Johan Bengtsson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  Metaxa2

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Mar 2. doi: 10.1111/1755-0998.12399.
metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
Bengtsson-Palme J1, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DG, Nilsson RH.

Antonie Van Leeuwenhoek. 2011 Oct;100(3):471-5. doi: 10.1007/s10482-011-9598-6. Epub 2011 Jun 15.
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH.

Cytoscape 3.7.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.7.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

mhsmm 0.4.16 – Parameter Estimation and Prediction for Hidden Markov and semi-Markov models for data with multiple Observation Sequences

mhsmm 0.4.16

:: DESCRIPTION

mhsmm is a software of parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. The software is suitable for equidistant time series data, with multivariate and/or missing data.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

  mhsmm

:: MORE INFORMATION

Citation

Jared O’Connell, Soren Hojsgaard (2011).
Hidden Semi Markov Models for Multiple Observation Sequences: The mhsmm Package for R.
Journal of Statistical Software, 39(4), 1-22.