rSPR 1.3.0 – Calculate Rooted Subtree-prune-and-regraft Distances and rooted agreement forest

rSPR 1.3.0

:: DESCRIPTION

rSPR (rooted subtree-prune-and-regraft) is a software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux
Perl
C++ Compiler

:: DOWNLOAD

rSPR

:: MORE INFORMATION

Citation

Whidden, C., Beiko, R.G., Zeh, N.
Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments.
In: Proceedings of the 9th International Symposium on Experimental Algorithms, SEA 2010. Lecture Notes in Computer Science, vol. 6049, pp. 141–153. Springer-Verlag (2010)

SPRSupertrees 1.2.1 – Calculate Rooted Supertrees that Minimize the SPR Distance.

SPRSupertrees 1.2.1

:: DESCRIPTION

SPR Supertrees is a software package for computing supertrees that minimize the SPR distance.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux
C++ Compiler

:: DOWNLOAD

SPRSupertrees

:: MORE INFORMATION

Citation

Whidden, C., Zeh, N., Beiko, R.G. (2013)
Supertrees based on the subtree prune-and-regraft distance.
PeerJ PrePrints 1:e18v1

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

DSSP 2.2.1 – Calculates DSSP Entries from PDB Entries

DSSP 2.2.1

:: DESCRIPTION

DSSP (Dictionary of protein secondary structure) is the program that calculates DSSP entries from PDB entries.

DSSP Online

::DEVELOPER

Wolfgang Kabsch and Chris Sander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

DSSP

:: MORE INFORMATION

Citation

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Kabsch W, Sander C,
Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824.

AutoMatrix – Calculate an Instantaneous Rate Matrix

AutoMatrix

:: DESCRIPTION

AutoMatrix is a Matlab script that will calculate an instantaneous rate matrix (and its eigen value decompostion for use in phylip programs) from a series of substitution count matrices calculated for different levels of sequence identity/similarity.

::DEVELOPER

The Tillier Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
MatLab

:: DOWNLOAD

AutoMatrix

:: MORE INFORMATION

Citation:

A transition probability model for amino acid substitutions from BLOCKS
Shalini Veerassamy, Andrew Smith and Elisabeth R. M. Tillier,
J. Computational Biology (2003) 10(6): 997-1010

Molecular Weight Calculator 1.0.1 – Calculate Molecular Weight or Molar Mass of any Chemical Formula

Molecular Weight Calculator 1.0.1

:: DESCRIPTION

Molecular Weight Calculator is an easy to use molecular weight calculator. Calculate molecular weight or molar mass of any chemical formula including hydrated molecules e.g MgSO4.7H2O. Insert elements from an embedded periodic table. Enter the formula in the scientific way same as know, as it is and calculate the molecular weight immediately.

::DEVELOPER

Chemiasoft

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Molecular Weight Calculator

:: MORE INFORMATION