AssemblX – Toolkit for Rapid and Reliable Multi-Gene Assemblies

AssemblX

:: DESCRIPTION

AssemblX toolkit allows the assembly of up to 25 transcriptional units, consisting of many more individual DNA fragments, on a single plasmid in the host Saccharomyces cerevisiae.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res, 45 (10), e80 2017 Jun 2
AssemblX: A User-Friendly Toolkit for Rapid and Reliable Multi-Gene Assemblies
Lena Hochrein , Fabian Machens , Juergen Gremmels , Karina Schulz , Katrin Messerschmidt , Bernd Mueller-Roebe

hapsembler 2.21 – Haplotype-specific Genome Assembly Toolkit

hapsembler 2.21

:: DESCRIPTION

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  hapsembler

:: MORE INFORMATION

Citation

Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.

MAVisto 2.7.0 – Motif Analysis and VISualisation TOolkit

MAVisto 2.7.0

:: DESCRIPTION

MAVisto (Motif Analysis and VISualisation TOolkit)is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 MAVisto

:: MORE INFORMATION

Citation

Schreiber, F. and Schwöbbermeyer H.
MAVisto: a tool for the exploration of network motifs.
Bioinformatics, 21, 3572-3574, 2005.

TST 1.4.3 – Tissue Simulation Toolkit

TST 1.4.3

:: DESCRIPTION

TST is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

::DEVELOPER

The Biomodeling and Biosystems Analysis Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

 TST

:: MORE INFORMATION

Citation

R M H Merks, & J A Glazier. (2005).
A cell-centered approach to developmental biology.
Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028.

DynaMIT 1.1.5 – Dynamic Motif Integration Toolkit

DynaMIT 1.1.5

:: DESCRIPTION

DynaMIT is a flexible platform for sequence and structure motifs integration, providing the means to execute multiple motif search tools, integrate their output and display the obtained results in a plethora of different ways.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 DynaMIT

:: MORE INFORMATION

Citation

DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A.
Nucleic Acids Res. 2015 Aug 7. pii: gkv807

DistMap 1.0 – A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

DistMap 1.0

:: DESCRIPTION

DistMap is a user-friendly pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Perl
  • Mapper executable
  •  MergeSamFiles.jar and SortSam.jar from PICARD (http://picard.sourceforge.net).
  • A working Hadoop cluster.

:: DOWNLOAD

 DistMap

:: MORE INFORMATION

Citation:

Pandey RV, Schlötterer C. (2013)
DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
PLoS One. 8(8):e72614.

BAMTOOLS 2.5.1 – C++ API and Toolkit for Analyzing and Managing BAM files

BAMTOOLS 2.5.1

:: DESCRIPTION

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BAMTOOLS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1691-2. Epub 2011 Apr 14.
BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, , Strömberg MP, Marth GT.

ITEP 1.1 – Integrated Toolkit for Exploration of Pan-genomes

ITEP 1.1

:: DESCRIPTION

ITEP is a suite of scripts and Python libraries for the comparison of microbial genomes. It includes tools for de novo protein family prediction by clustering, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, cluster curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Python

:: DOWNLOAD

 ITEP

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8.
ITEP: an integrated toolkit for exploration of microbial pan-genomes.
Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND1.

CRAVAT 4.0 – Cancer-related Analysis of Variants Toolkit

CRAVAT 4.0

:: DESCRIPTION

CRAVAT is a web server with simple interface where cancer-related analysis of variants are performed.CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CRAVAT: cancer-related analysis of variants toolkit.
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.
Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.