Kaks_Calculator 2.0 – Calculate Ka and Ks through Model Selection and Model Averaging

Kaks_Calculator 2.0

:: DESCRIPTION

KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator.

::DEVELOPER

The National Genomics Data Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 KaKs_Calculator

:: MORE INFORMATION

Citation:

Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80. doi: 10.1016/S1672-0229(10)60008-3.
KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.
Wang D1, Zhang Y, Zhang Z, Zhu J, Yu J.

Zhang Zhang, Jun Li,Xiao-QianZhao,etal.
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging
Geno. Prot. Bioinfo.,2006,4(4)

MultiGeMS 1.0 – Detection of SNVs from Multiple Samples Using Model Selection on High-Throughput Sequencing Data

MultiGeMS 1.0

:: DESCRIPTION

MultiGeMS (Multi-sample Genotype Model Selection) is a multiple sample single nucleotide variant (SNV) caller that works with alignment files of high-throughput sequencing (HTS) data. MultiGeMS calls SNVs based on a statistical model selection procedure and accounts for enzymatic substitution sequencing errors.

::DEVELOPER

Cui Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MultiGeMS

:: MORE INFORMATION

Citation

MultiGeMS: Detection of SNVs from Multiple Samples Using Model Selection on High-Throughput Sequencing Data.
Murillo G, You N, Su X, Cui W, Reilly MP, Li M, Ning K, Cui X.
Bioinformatics. 2016 Jan 18. pii: btv753

ABC-SysBio 2.08 – Parameter Inference and Model Selection

ABC-SysBio 2.08

:: DESCRIPTION

ABC-SysBio (approximate Bayesian computation) implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML). ABC-SysBio is a Python package that combines three algorithms: ABC rejection sampler, ABC SMC for parameter inference and ABC SMC for model selection.

::DEVELOPER

The research in the Theoretical Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 ABC-SysBio

:: MORE INFORMATION

Citation:

J. Liepe, C. Barnes, E. Cule, K. Erguler, P. Kirk, T. Toni, M. P.H. Stumpf
ABC-SysBio – Approximate Bayesian Computation in Python with GPU support
Bioinformatics. 2010 Jul 15;26(14):1797-9.

ParGenes 1.1.0 – Model Selection and Tree Inference on thousands of Genes

ParGenes 1.1.0

:: DESCRIPTION

ParGenes is a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes, using ModelTest-NG and RAxML-NG.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

ParGenes

:: MORE INFORMATION

Citation

Bioinformatics. 2019 May 15;35(10):1771-1773. doi: 10.1093/bioinformatics/bty839.
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.
Morel B, Kozlov AM, Stamatakis A.