Tag: Landscape

AgIn 0.9 – Measuring the landscape of CpG methylation of individual Repetitive Elements

AgIn 0.9

:: DESCRIPTION

AgIn (Aggregate on Intervals) processes SMRT sequencing kinetic summary to predict regional methylation on large genome.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AgIn

:: MORE INFORMATION

Citation

Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S.
AgIn: measuring the landscape of CpG methylation of individual repetitive elements.
Bioinformatics. 2016 Oct 1;32(19):2911-9. doi: 10.1093/bioinformatics/btw360. Epub 2016 Jun 17. PMID: 27318202; PMCID: PMC5039925.

GETUTR 2.0.0 – Global Estimation of the 3′ UTR landscape based on RNA sequencing

GETUTR 2.0.0

:: DESCRIPTION

GETUTR provides a landscape of 3′ UTR from RNA-seq data. It has three steps: preprocessing, smoothing and normalization.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GETUTR

:: MORE INFORMATION

Citation:

Global Estimation of the 3′ Untranslated Region Landscape Using RNA Sequencing.
Kim M, You BH, Nam JW.
Methods. 2015 Apr 18. pii: S1046-2023(15)00157-7. doi: 10.1016/j.ymeth.2015.04.011.

Spatial 1.0.0 – Model Animal Movement on Landscapes

Spatial 1.0.0

:: DESCRIPTION

Spatial is an agent-based model of the movements of animals on landscapes. The landscapes can be entered from image files or from tables of data. Rules are entered to describe the attractiveness, permeability, and rate of movement of animals for each landscape feature (optionally including other animals). Spatial then simulates the movements over time, and dsiplays final location, tracks, or density of occupancy.

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Spatial 

:: MORE INFORMATION

Xscape – Tools for Maximum-Parsimony Phylogenetic Tree Reconciliation over the Event Cost Landscape

Xscape

:: DESCRIPTION

Xscape is a set of Python tools for maximum parsimony phylogenetic event-based tree reconciliation in undated trees using the DTL (duplication-loss-transfer) model with applications to gene trees and species trees; parasite trees and host trees; and species trees and area cladograms.

::DEVELOPER

Ran Libeskind-Hadas

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Python
  • matplotlib
  • BioPython

:: DOWNLOAD

 Xscape

:: MORE INFORMATION

Citation

Pareto-optimal phylogenetic tree reconciliation.
Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M.
Bioinformatics. 2014 Jun 15;30(12):i87-i95. doi: 10.1093/bioinformatics/btu289.

Xlandscape 1.0 – X-window Sequence Landscape program

Xlandscape 1.0

:: DESCRIPTION

Xlandscape provides a graphical interface for the generation, display and manipulation of a sequence landscape that will run on all X-windows-based Unix workstations.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

Xlandscape

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Xlandscape

:: MORE INFORMATION

Citation

Bioinformatics. 1998;14(1):74-80.
Xlandscape: the graphical display of word frequencies in sequences.
Levy S, Compagnoni L, Myers EW, Stormo GD.

iMCMC – Illustrate Markov chain Monte Carlo (MCMC) for a Simple Landscape

iMCMC

:: DESCRIPTION

iMCMC is a Macintosh application that illustrates Markov chain Monte Carlo (MCMC) for a simple landscape.

::DEVELOPER

John Huelsenbeck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Macintosh

:: DOWNLOAD

 iMCMC

:: MORE INFORMATION