Tag: sampling

SUGEN v8.1 – Genetic Association Analysis Under Complex Survey Sampling

SUGEN v8.1

:: DESCRIPTION

SUGEN is a command-line software program written in C++ to implement the weighted and unweighted approaches for various types of association analysis under complex survey sampling.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

SUGEN

:: MORE INFORMATION

Citation

Lin DY, Tao R, Kalsbeek WD, Zeng D, Gonzalez F 2nd, Fernández-Rhodes L, Graff M, Koch GG, North KE, Heiss G.
Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos.
Am J Hum Genet. 2014 Dec 4;95(6):675-88. doi: 10.1016/j.ajhg.2014.11.005. PMID: 25480034; PMCID: PMC4259979.

Ringer – Detect Molecular Motions by automatic Electron Density Sampling

Ringer

:: DESCRIPTION

The program Ringer detects molecular motions by automatic electron density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which part are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design.

::DEVELOPER

Alber Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Ringer

:: MORE INFORMATION

Citation

Lang et al.
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
Protein Sci.: 2010, 19(7);1420-31.

DLTCount – Counting and Sampling Gene Family Histories

DLTCount

:: DESCRIPTION

DLTCount : Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DLTCount

:: MORE INFORMATION

Citation

Chauve C, Ponty Y, Wallner M.
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.
J Math Biol. 2020 Apr;80(5):1353-1388. doi: 10.1007/s00285-019-01465-x. Epub 2020 Feb 15. PMID: 32060618; PMCID: PMC7052048.

Core Hunter 3.2.0 – A Program for Sampling Genetic Resources

Core Hunter 3.2.0

:: DESCRIPTION

Core Hunter is a program for sampling genetic resources. Users can specify the sampling intensity and which genetic measures will be used for selection criteria. For instance, a core subset could be selected that best maximizes the average modified Rogers’ distance, or one that maximizes the Shannon’s diversity index. Users can also maximize multiple genetic measures simultaneously, by specifying a weight for each required measure.

::DEVELOPER

Core Hunter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 Core Hunter

:: MORE INFORMATION

Citation

De Beukelaer H, Davenport GF, Fack V.
Core Hunter 3: flexible core subset selection.
BMC Bioinformatics. 2018 May 31;19(1):203. doi: 10.1186/s12859-018-2209-z. PMID: 29855322; PMCID: PMC6092719.

BMC Bioinformatics. 2012 Nov 23;13:312. doi: 10.1186/1471-2105-13-312.
Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search.
De Beukelaer H, Smykal P, Davenport GF, Fack V.

optGpSampler 1.1 – Sampling Constraint-based Genome-scale Metabolic Networks

optGpSampler 1.1

:: DESCRIPTION

OptGpSampler is a parallel implementation of the Artificial Centering Hit-and-Run algorithm. With this tool, you can efficiently sample the steady-state solution space of a metabolic network.

::DEVELOPER

optGpSampler team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • MatLab
  • Python

:: DOWNLOAD

  optGpSampler

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 14;9(2):e86587. doi: 10.1371/journal.pone.0086587. eCollection 2014.
optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks.
Megchelenbrink W, Huynen M, Marchiori E

MOSAICS 4.0 / PymoSAICS 0.2.0 – Methodologies for Optimization and SAmpling In Computational Studies

MOSAICS 4.0 / PymoSAICS

:: DESCRIPTION

MOSAICS is a sampling program developed to improve sampling efficiency by incorporating natural move-sets for proteins and nucleic acids.

MOSAICS-EM is a software package designed to refine molecular conformations directly against two-dimensional (2D) electron-microscopy images.

PymoSAICS is a pyMol plugin of MOSAICS.

::DEVELOPER

MOSAICS team

:: SCREENSHOTS

PymoSAICS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Python
  • pyMOL

:: DOWNLOAD

 MOSAICS / PymoSAICS

:: MORE INFORMATION

Citation

Exploring peptide/MHC detachment processes using Hierarchical Natural Move Monte Carlo.
Knapp B, Demharter S, Deane CM, Minary P.
Bioinformatics. 2015 Sep 22. pii: btv502

RNA-WL 1.5 – Thermodynamics of RNA structures by Wang-Landau sampling

RNA-WL 1.5

:: DESCRIPTION

RNA-WL is an implementation of the Wang-Landau non-Boltzmannian sampling algorithm to approximate the partition function for RNA secondary structures.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • WebServer
  • C Compiler

:: DOWNLOAD

 RNA-WL

:: MORE INFORMATION

Citation:

Feng Lou, Peter Clote.
Thermodynamics of RNA structures by Wang-Landau sampling.
ISMB 2010, Bioinformatics 2010 Jun 15;26(12):i278-86

ChainTweak – Sampling from the Neighbourhood of a Protein Conformation

ChainTweak

:: DESCRIPTION

ChainTweak is a program for sampling the neighbourhood of a given protein backbone. It poses the problem of finding conformations which have the same bond lengths, bond angles but are within a few Angstrom (say 4A) of the original conformation. It does this by using sliding window approach to perform local modifications to the structure without modifying the distal ends.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ChainTweak

:: MORE INFORMATION

Citation:

Pac Symp Biocomput. 2005:52-63.
Chaintweak: sampling from the neighbourhood of a protein conformation.
Singh R, Berger B.

TWIGS – Three-Way module Inference via Gibbs Sampling

TWIGS

:: DESCRIPTION

TWIGS is a tool for advanced analysis of three-way data (e.g., patient-gene-time in gene expression or subject-voxel-time in fMRI). TWIGS identifies both core modules that appear in multiple patients and patient-specific augmentations of these core modules that contain additional genes.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 TWIGS

:: MORE INFORMATION

Citation

A hierarchical Bayesian model for flexible module discovery in three-way time-series data.
Amar D, Yekutieli D, Maron-Katz A, Hendler T, Shamir R.
Bioinformatics. 2015 Jun 15;31(12):i17-i26. doi: 10.1093/bioinformatics/btv228.

Sampbias – Sampling Bias in Species Distribution Records

Sampbias

:: DESCRIPTION

Sampbias is a method and tool to 1) visualize the distribution of occurrence records and species in any user-provided dataset, 2) quantify the biasing effect of geographic features related to human accessibility, such as proximity to cities, rivers or roads, and 3) create publication-level graphs of these biasing effects in space.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • R

:: DOWNLOAD

Sampbias

:: MORE INFORMATION