jagn 1.02 – Java-Based Model for Artificial Gene Networks Generation

jagn 1.02

:: DESCRIPTION

jagn is a software for an Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data, which can be used by computational methods to recover the network topology, and then, analyse the results based on complex networks measurements/topology.

::DEVELOPER

Fabrício Martins Lopes

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

jagn

:: MORE INFORMATION

Citation:

Lopes, Fabrício M.; Cesar-Jr, Roberto M.; Costa, Luciano da F.
Gene expression complex networks: synthesis, identification and analysis.
Journal of Computational Biology, v. 18, p. 1353-1367, 2011.

IBDNe 20200423 – Estimate Effective Population size in recent Generations

IBDNe 20200423

:: DESCRIPTION

The IBDNe program estimate ancestry-specific historical effective population size.

::DEVELOPER

Brian L. Browning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

IBDNe

:: MORE INFORMATION

Citation:

Browning SR, Browning BL.
Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.
Am J Hum Genet. 2015 Sep 3;97(3):404-18. doi: 10.1016/j.ajhg.2015.07.012. Epub 2015 Aug 20. PMID: 26299365; PMCID: PMC4564943.

TagGD – DNA Tag Generation and Demultiplexing

TagGD

:: DESCRIPTION

TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy.

::DEVELOPER

the Science for Life Laboratory, Uppsala University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows

:: DOWNLOAD

TagGD

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e57521. doi: 10.1371/journal.pone.0057521. Epub 2013 Mar 4.
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P.

Pajek Writer – Generation of Structural Representation of Biochemical Processes in Format Pajek

Pajek Writer

:: DESCRIPTION

Pajek Writer – software for generation of structural representation of biochemical processes in format Pajek on a set of the proceeding reactions presented in the form of the list of biochemical reactions.

::DEVELOPER

Biomodels Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
Java

:: DOWNLOAD

Pajek Writer

:: MORE INFORMATION

AgeStructure 1.0 – Estimate Effective Size & Generation Interval of Population with overlapping Generations

AgeStructure 1.0

:: DESCRIPTION

AgeStructure is a computer program for estimating the generation interval, effective size, variances and covariances of lifetime number of offspring of an age structured population with overlapping generations.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Fortran 90/95 compiler

:: DOWNLOAD

AgeStructure

:: MORE INFORMATION

Citation

Wang, J., Brekke, P. , Huchard, E., Knapp, L. A. , Cowlishaw, G. 2010.
Estimation of parameters of inbreeding and genetic drift in populations with overlapping generations.
Evolution, 64, 1704–1718.

systemPipeR 1.27.27 – NGS Workflow and report Generation Environment

systemPipeR 1.27.27

:: DESCRIPTION

systemPipeR is an R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux/ MacOsX/Windows
R package
BioConductor

:: DOWNLOAD

systemPipeR

:: MORE INFORMATION

Citation

H Backman TW, Girke T.
systemPipeR: NGS workflow and report generation environment.
BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0. PMID: 27650223; PMCID: PMC5029110.

MOLGEN 5.0 – Molecular Structure Generation

MOLGEN 5.0

:: DESCRIPTION

The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures. The project arose in 1985 from the idea to provide an efficient and portable tool for molecular structure elucidation in chemical industry, research, and education.

::DEVELOPER

MOLGEN Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

MOLGEN

:: MORE INFORMATION

R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rücker, A. Wassermann :
MOLGEN 5.0, a Molecular Structure Generator.
Submitted to Bentham Science Publishers Ltd. 2012

PhyloPro – Generation and Visualization of Phylogenetic Profiles across Eukarya

PhyloPro

:: DESCRIPTION

PhyloPro allows the user to rapidly identify core conserved elements of biological processes together with those that may represent lineage-specific innovations.

::DEVELOPER

Parkinson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):877-8. doi: 10.1093/bioinformatics/btr023. Epub 2011 Jan 19.
PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya.
Xiong X, Song H, On T, Lochovsky L, Provart NJ, Parkinson J.

WhatsHap – Haplotype Assembly for Future-Generation Sequencing Reads

WhatsHap

:: DESCRIPTION

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

::DEVELOPER

The Algorithms for Computational Genomics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
C++

:: DOWNLOAD

WhatsHap

:: MORE INFORMATION

Citation

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.
J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157

DecoyDatabaseBuilder 1.5.47 – Generation of Decoy Sequences for Amino Acid Databases

DecoyDatabaseBuilder 1.5.47

:: DESCRIPTION

DecoyDatabaseBuilder is a module of the PeakQuant suite, it enables the generation of decoy sequences for amino acid databases.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
JRE

:: DOWNLOAD

DecoyDatabaseBuilder

:: MORE INFORMATION

Citation

Proteomics. 2008 Mar;8(6):1129-37. doi: 10.1002/pmic.200701073.
An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications.
Reidegeld KA1, Eisenacher M, Kohl M, Chamrad D, Körting G, Blüggel M, Meyer HE, Stephan C.