:: DESCRIPTION
Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.
::DEVELOPER
Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof
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:: MORE INFORMATION
Citation
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321
:: DESCRIPTION
RocketBugs is a simulation of the actin-based motility of Listeria monocytogenes.
RocketBugsRender is a special rendering and graphing program for the simulation output of “RocketBugs”, the actin-based Listeria motility simulations
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Susanne M. Rafelski, Jonathan B. Alberts, Garrett M. Odell
An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility
PLoS Comput Biol 5(7): e1000434. doi:10.1371/journal.pcbi.1000434
:: DESCRIPTION
ParMSpindle is a 3D, force-based simulation of the ParM mediated segregation of bacterial plasmids, tracking the biochemical state of each monomer with experimentally determined filament dynamics
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N/A
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:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BATMAN-TCM is an online bioinformatics analysis tool specially designed for the research of molecular mechanism of TCM.
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:: SCREENSHOTS
N/A
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:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H, Diao L, Gu J, Wang W, Li D, He F.
BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine.
Sci Rep. 2016 Feb 16;6:21146. doi: 10.1038/srep21146. PMID: 26879404; PMCID: PMC4754750.
:: DESCRIPTION
SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.
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:: REQUIREMENTS
:: DOWNLOAD
SimPlot if you cannot make that work, please email me for a download link
:: MORE INFORMATION
Reference to the paper in which author first described SimPlot
Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.
:: 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).
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:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.
:: DESCRIPTION
VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.
:: DESCRIPTION
MargFreq is a relatively user-friendly Windows program that does a repetitive task – calculating the marginal frequencies at each position of a nucleotide/amino acid sequence. This program accepts sequence alignments in many different formats. It also does some rudimentary analysis for covariation.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.
:: DESCRIPTION
CleanCollapse is a relatively user-friendly Windows program that accepts an alignment of sequences, and optionally can remove rare sporadic polymorphisms that may represent analytical artifacts, and also reduce redundancy by “collapsing” identical sequences into a single sequence. The program provides a record of these manipulation, and some rudimentary analysis (e.g. proportion of synonymous and nonsynonymous sporadic changes) that may assist interpretation
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.