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Protocols

Simprot specifications

Information


Unique identifier OMICS_15377
Name Simprot
Interface Web user interface
Restrictions to use None
Input data A tree file.
Input format NEWICK
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Elisabeth Tillier

Information


Unique identifier OMICS_15377
Name Simprot
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A tree file.
Input format NEWICK
Operating system Unix/Linux, Windows
Programming languages C++
License Other
Computer skills Advanced
Version 1.03
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Elisabeth Tillier

Publication for Simprot

Simprot citations

 (4)
library_books

Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

2014
Evol Bioinform Online
PMCID: 4267518
PMID: 25574120
DOI: 10.4137/EBO.S19199

[…] is also logged. rose incorporates indels linearly in accordance with the evolutionary distance and length distribution. indel models with nonlinear indel probabilities cannot be shown in rose. simprot is another simulation tool that incorporates indels; however, it does not support the feature of root sequence as an input, the conservation of motifs or modifying amino acid frequencies […]

library_books

Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

2012
PLoS One
PMCID: 3473043
PMID: 23091608
DOI: 10.1371/journal.pone.0047108

[…] are somehow biased by the particular program (in this case msavolve) used to simulate the msas. for this reason, we also simulated 100 msas for each of the 8 families using an earlier program, simprot, developed by one of us , which is based on a simulation strategy completely different from that of msavolve. in these simulations, there is no recombination between fragments […]

library_books

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

2008
Genome Biol
PMCID: 2760874
PMID: 18840304
DOI: 10.1186/gb-2008-9-10-r147

[…] processes without indels; a recent example, which generates data of a given dinucleotide content (with a somewhat constrained choice of substitution model), is sissiz []. protein simulators include simprot [], indel-seq-gen [] and evolveagene []; of these, indel-seq-gen offers the most realism, with rate heterogeneity and a diverse set of mutations. simulators for genomic sequence (including […]

library_books

The accuracy of several multiple sequence alignment programs for proteins

2006
BMC Bioinformatics
PMCID: 1633746
PMID: 17062146
DOI: 10.1186/1471-2105-7-471

[…] to gauge the relative accuracy of the programs., we tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software simprot which creates known alignments under realistic and controlled evolutionary scenarios. we have simulated more than 30000 alignment sets using various evolutionary histories in order to define […]


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Simprot institution(s)
Ontario Cancer Institute, University Health Network, Toronto, ON, Canada; Department Medical Biophysics, University of Toronto, Toronto, ON, Canada; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
Simprot funding source(s)
Supported by CIHR and Genome Canada.

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