Tag: Calculate

VisSPA 1.62 – Calculate Frequency of Residues

VisSPA 1.62

:: DESCRIPTION

VisSPA (Visual Signature Pattern Analysis) is a program that accepts an alignment of sequences, interactively analyzes frequencies of residues at each position in groups of sequences and supports the generation of sequence logos. The frequency calculations and program name were initially inspired by VESPA (by Gerry Myers and Bette Korber of Los Alamos National Labs).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VisSPA

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

ENCprime 20140112 – Calculate Codon Usage Bias summary statistic, Nc’

ENCprime 20140112

:: DESCRIPTION

ENCprime is a program that calculates a codon usage bias summary statistic, Nc’. It is based on the effective number of codons statistic Nc (or ENC) developed by Frank Wright, but improves upon it by accounting for background nucleotide composition.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  ENCprime

:: MORE INFORMATION

KinInfor v1 – Calculate Informativeness of Markers in Inferring Pairwise Relatedness

KinInfor v1

:: DESCRIPTION

KinInfor (Kinship Informativeness) is a Fortran program that calculates the informativeness of markers in inferring pairwise relatedness or relationships.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Fortran 90/95 compiler

:: DOWNLOAD

  KinInfor

:: MORE INFORMATION

Citation

Wang, J (2006)
Informativeness of genetic markers for pairwise relationship and relatedness inference.
Theoretical Population Biology 70:300-321.

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)

MiniInbred 2.1 – Calculate and Minimize Inbreeding Coefficients

MiniInbred 2.1

:: DESCRIPTION

MiniInbred predicts inbreeding levels in the next generation by identifying matings that yield the lowest inbreeding level in the offspring. The inbreeding coefficients resulting from all potential matings of the current breeding animals (generation 1) are calculated, and the potential matings among the current breeding animals that yield the lowest inbreeding level are identified. The program also predicts the lowest inbreeding available in the third generation. In this case, the hypothetical offspring (generation 2) of the current breeding animals are treated as ‘parents’, and the inbreeding coefficients resulting from all potential matings between the hypothetical ‘parents’ are calculated, and the potential matins among the hypothetical ‘parents’ that minimize inbreeding are identified.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows / Linux

:: DOWNLOAD

 MiniInbred

:: MORE INFORMATION

gKaKs 1.3.0 – Genome level calculate Ka/Ks

gKaKs 1.3.0

:: DESCRIPTION

gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs can automatically detect and eliminate frameshift mutations and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset.

::DEVELOPER

Fan Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 gKaKs

:: MORE INFORMATION

Citation

Chengjun Zhang; Jun Wang; Manyuan Long; Chuanzhu Fan
gKaKs: The pipeline for genome level Ka/Ks calculation.
Bioinformatics (2013) 29 (5): 645-646.; doi: 10.1093/bioinformatics/btt009

Molar Mass Calculator 1.3 – Calculate Chemical Formula Molar Mass

Molar Mass Calculator 1.3

:: DESCRIPTION

Molar Mass Calculator calculats chemical formula molar mass  by adding up the individual molar masses of its constituent elements. Given a chemical formula this iPad app will calculate molar mass and subtotal masses for the substance.

::DEVELOPER

Thundercloud Consulting, LLC

:: SCREENSHOTS

:: REQUIREMENTS

  • iOS

:: DOWNLOAD

 Molar Mass Calculator

:: MORE INFORMATION

TM-score 20190822 – Calculate Similarity of Topologies of two Protein Structures

TM-score 20190822

:: DESCRIPTION

TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TM-score

:: MORE INFORMATION

Citation

J. Xu, Y. Zhang,
How significant is a protein structure similarity with TM-score=0.5?
Bioinformatics, 2010 26, 889-895

K-Estimator 6.1v – Calculate the number of Nucleotide Substitutions

K-Estimator 6.1v

:: DESCRIPTION

K-Estimator is a software that estimates the number of of synonymous (Ks) and nonsynonymous substitutions (Ka) per site (divergence) when comparing two aligned nucleotide sequences, both protein-coding and non-coding. Confidence intervals of the divergence estimates are obtained by Monte Carlo simulation.

::DEVELOPER

Josep M. Comeron

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

K-Estimator

:: MORE INFORMATION

Citation

Comeron JM. (1999)
K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals.
Bioinformatics 15(9):763-764.

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