Tag: Selection

ProtTest 3.3 – Selection of Best-fit Models of Protein Evolution

ProtTest 3.3

:: DESCRIPTION

ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ProtTest

:: MORE INFORMATION

Citation:

Darriba D, Taboada GL, Doallo R, Posada D.
ProtTest 3: fast selection of best-fit models of protein evolution.
Bioinformatics (2011)doi: 10.1093/bioinformatics/btr088

MEDUSA – Selection and Visual Assessment of PCR Primer Pair

MEDUSA

:: DESCRIPTION

MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

 MEDUSA

:: MORE INFORMATION

Citation

Bioinformatics. 2001 Jul;17(7):656-7.
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Podowski RM, Sonnhammer EL.

mbs 2 – Generating Samples of DNA Sequences with a Biallelic site under Selection

mbs 2

:: DESCRIPTION

mbs is a simulation program to generate patterns of single nucleotide polymorphism (SNP) data in a region that is linked to a biallelic site targeted by selection. The software was developed by modifying the commonly used Hudson’s ms simulator

::DEVELOPER

the INNAN Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 mbs

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 May 30;10:166. doi: 10.1186/1471-2105-10-166.
mbs: modifying Hudson’s ms software to generate samples of DNA sequences with a biallelic site under selection.
Teshima KM, Innan H.

MSMS 3.2rcb122 / MSMSPlay – Coalescent Simlation tool with Selection / Exploration of Basic Population Genetic Theory

MSMS 1.3 / MSMSPlay

:: DESCRIPTION

MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios.

MSMSPlay is a GUI designed for simple exploration of basic population genetic theory. Its meant for exploratory runs with some useful output in an interactive fashion.

::DEVELOPER

The Mathematics and BioSciences Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MSMS / MSMSPlay

:: MORE INFORMATION

Citation

Ewing G. and Hermisson J. (2010).
MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus.
Bioinformatics 26: 2064-2065.

Selection 3.2 – Demonstrate Simple Population Genetic Effects of Selection

Selection 3.2

:: DESCRIPTION

Selection is a simulation program which demonstrates simple population genetic effects of selection, mutation, migration and drift in a single-locus, two-allele model. The program offers both an analytic and a stochastic model with full user control of the simulation parameters and a variety of options in the onscreen display. Students can control the relative fitnesses of the two alleles, mutation and migration rates, as well as population size. The display can be set to overlay multiple simulation runs, and the scale can be altered to view different parts of a given simulation run in greater detail.

::DEVELOPER

The Queller/Strassmann Research Group at Washington University in St. Louis

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac

:: DOWNLOAD

 Selection

:: MORE INFORMATION

Tagger – Selection and Evaluation of tag SNPs

Tagger

:: DESCRIPTION

Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

P.I.W. de Bakker, R. Yelensky, I. Pe’er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005)
Efficiency and power in genetic association studies.
Nature Genetics. 37: 1217-1223

codonbias 20060818 – Estimate Selection Coefficients relating to optimal Codon usage

codonbias 20060818

:: DESCRIPTION

codonbias will allow the user to estimate selection coefficients relating to optimal codon usage. The basic methodology is similar to the codon based models implemented in the popular program PAML by Ziheng Yang. However, it explicitly models selection for optimal codon usage on different lineages of a phylogeny.

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 codonbias

:: MORE INFORMATION

SELECTpro 1.0 – Protein Model Scoring/Selection and Side-Chain Prediction

SELECTpro 1.0

:: DESCRIPTION

SELECTpro is a novel structure-based model selection method derived from an energy function comprising physical, statistical, and predicted structural terms. Novel and unique energy terms include predicted secondary structure, predicted solvent accessibility, predicted contact map, beta-strand pairing, and side-chain hydrogen bonding.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SELECTpro

:: MORE INFORMATION

Citation:

A. Randall, P. Baldi.
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.
BMC Structural Biology, 8, 52, 2008

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