MAXPROC – Calculate Maximum Likelihood Estimates of Linkage Parameters

MAXPROC

:: DESCRIPTION

MAXPROC calculates maximum likelihood estimates of linkage parameters under heterogeneity and their standard errors using EM and SEM algorithms

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MAXPROC

:: MORE INFORMATION

Citation

Biswas S and Lin S (2003).
Evaluation of maximization procedures for estimating linkage parameters under heterogeneity.
Genetic Epidemiology, 26, 206-217.

MSTgold 2.5 – Calculates Minimum Spanning Trees

MSTgold 2.5

:: DESCRIPTION

MSTgold calculates minimum spanning trees (MST) from protein and nucleotide sequences, from binary characters and SNPs, and from tab-delimited data such as microsatellite data. It also estimates the number of different MSTs from a data set, bootstraps MSTs, and identifies the most reliable tree among a set of equal-length MSTs.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 MSTgold

:: MORE INFORMATION

Citation

Stephen J. Salipante and Barry G. Hall
Inadequacies of Minimum Spanning Trees in Molecular Epidemiology
J. Clin. Microbiol. October 2011 vol. 49 no. 10 3568-3575

GrowthRates 4.0 – Calculates Bacterial Growth Rates

GrowthRates 4.0

:: DESCRIPTION

GrowthRates is a program that calculates bacterial growth rates from the data generated by a micro-plate reader used to monitor the growth of bacterial cultures in micro-plate wells. The program automatically identifies the exponential phase of the growth curve and uses that portion of the curve to calculate growth rates and std. errors of those rates

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GrowthRates

:: MORE INFORMATION

Citation

Statistical Package for Growth Rates Made Easy.
Mira P, Barlow M, Meza JC, Hall BG.
Mol Biol Evol. 2017 Dec 1;34(12):3303-3309. doi: 10.1093/molbev/msx255.

AVP 1.3 – Calculate Protein Void Volumes and Packing Quality

AVP 1.3

:: DESCRIPTION

AVP (Another Void Program) is a new method for the analysis of voids in proteins and packing quality in a single united program. Traditionally been analysed using different approaches, but in reality they are extremes of the same phenomenon – imperfect packing of atoms in the inside of a protein.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AVP

:: MORE INFORMATION

Torsions – Calculates Backbone Torsion Angles from a PDB file

Torsions

:: DESCRIPTION

TORSIONS is a simple program to read a PDB file and calculate backbone torsion angles. It calculates phi, psi and omega and can also calculate C-alpha pseudo-torsions.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Torsions

:: MORE INFORMATION

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.

Molar Mass Calculator 1.1.1 – Calculate Chemical Formula Molar Mass

Molar Mass Calculator 1.1.1

:: 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

MolarMass

:: REQUIREMENTS

  • iOS

:: DOWNLOAD

 Molar Mass Calculator

:: 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

THE MANYUAN LONG LABORATORY , 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

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

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

BGI

:: 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)