Tag: Analysis

SVAMP 2.10 – Sequence Variation Analysis,Maps and Phylogeny

SVAMP 2.10

:: DESCRIPTION

SVAMP is standalone desktop application to visualise variants (SNPs and indels) and peform realtime analysis on selected regions of a genome on specific samples. SVAMP has some interesting features like phylogeography,allele frequency map and principal coordinate analysis.

::DEVELOPER

Computational Bioscience Research Center,  King Abdullah University of Science and Technology

:: SCREENSHOTS

SVAMP

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 SVAMP

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 23. [Epub ahead of print]
SVAMP: sequence variation analysis, maps and phylogeny.
Naeem R1, Hidayah L, Preston MD, Clark TG, Pain A.

Pyicoteo 2.0.7 – Analysis of High-throughput Sequencing data

Pyicoteo 2.0.7

:: DESCRIPTION

Pyicoteo is a suite of tools for the analysis of high-throughput sequencing data. It works with genomic coordinates, it was mainly developed using Solexa/Illumina mapped reads, but in its core it is platform-agnostic.

::DEVELOPER

Eyras Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 Pyicoteo

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 15;27(24):3333-40. Epub 2011 Oct 12.
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E.

ANAT 3.0 – Inference and Analysis of Functional Networks of Proteins

ANAT 3.0

:: DESCRIPTION

ANAT (Advanced Network Analysis Tool) , is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models

::DEVELOPER

Prof. Roded Sharan

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ANAT

:: MORE INFORMATION

Citation

Signorini LF, Almozlino T, Sharan R.
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches.
BMC Bioinformatics. 2021 Oct 27;22(1):526. doi: 10.1186/s12859-021-04449-1. PMID: 34706638.

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks.
N. Yosef, E. Zalckvar, A. D. Rubinstein, M. Homilius, N. Atias, L. Vardi, I. Berman, H. Zur, A. Kimchi, E. Ruppin and R. Sharan
Sci. Signal. 4, pl1 (2011).

Rainbow beta 1.2 – Toolbox for Phylogenetic Supertree Construction & Analysis

Rainbow beta 1.2

:: DESCRIPTION

Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science , Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Rainbow

:: MORE INFORMATION

Citation

D. Chen, O. Eulenstein and D. Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Bioinformatics (2004) 20 (16): 2872-2873.

BIC-seq 2 0.2.4 – Copy Number analysis from Whole-genome Sequencing data

BIC-seq 2 0.2.4

:: DESCRIPTION

BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package / Perl

:: DOWNLOAD

 BIC-seq

:: MORE INFORMATION

Citation

Xi et al,
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
PNAS, 2011 November 15, 2011 vol. 108 no. 46

FASTRUCT 1.01 – Analysis of Population Genetics and Individual Assignment

FASTRUCT 1.01

:: DESCRIPTION

FASTRUCT is a non-Bayesian implementation of the classical model with no-admixture uncorrelated allele frequencies. This new program relies on the Expectation-Maximization principle, and produces assignment rivaling other model-based clustering programs. In addition, it can be several-fold faster than Bayesian implementations. The software consists of a command-line engine, which is suitable for batch-analysis of data, and a MS Windows graphical interface, which is convenient for exploring data.

::DEVELOPER

the Computational and Mathematical Biology group in Grenoble

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FASTRUCT

:: MORE INFORMATION

Citation

Chen C, Forbes F, François O (2006)
FASTRUCT: Model-based clustering made faster.
Molecular Ecology Notes Volume 6, Issue 4, pages 980–983,

MEGAN 6.21.14 – Metagenome analysis

MEGAN 6.21.14

:: DESCRIPTION

MEGAN (MEta Genome ANalyzer) allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 MEGAN

:: MORE INFORMATION

Citation

Analysis of 16S rRNA environmental sequences using MEGAN.
Mitra S, Stärk M, Huson DH.
BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17.

R-SAP 1.1 – RNA-Seq Analysis pipeline

R-SAP 1.1

:: DESCRIPTION

 R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values.

::DEVELOPER

McDonald Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 R-SAP

:: MORE INFORMATION

Citation:

Mittal VK, McDonald JF. 2012.
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.
Nucleic Acid Reseaech. Jan. 28;

AltAnalyze 2.1.4.3 – Microarry and RNA-Seq Analysis

AltAnalyze 2.1.4.3

:: DESCRIPTION

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

::DEVELOPER

the Nathan Salomonis laboratory at Cincinnati Children’s Hosptial Medical Center and the University of Cincinnati.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Python

:: DOWNLOAD

 AltAnalyze

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62. Epub 2010 May 31.
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M.

ISAMBARD v2.3.1 – Intelligent System for Analysis, Model Building And Rational Design of Biomolecules

ISAMBARD v2.3.1

:: DESCRIPTION

ISAMBARD is a Python-based framework for structural analysis and rational design of biomolecules, with a particular focus on parametric modelling of proteins.

::DEVELOPER

Woolfson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ISAMBARD

:: MORE INFORMATION

Citation

Wood CW, Heal JW, Thomson AR, Bartlett GJ, Ibarra AÁ, Brady RL, Sessions RB, Woolfson DN.
ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.
Bioinformatics. 2017 Oct 1;33(19):3043-3050. doi: 10.1093/bioinformatics/btx352. PMID: 28582565; PMCID: PMC5870769.

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