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SimPhy specifications

Information


Unique identifier OMICS_13198
Name SimPhy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Species or locus tree
Input format NEXUS
Output data Outputs consist of sequence alignments and a relational database that facilitate posterior analyses. SimPhy includes also a species tree file, a locus tree file with all the locus trees, and one gene tree file per locus tree (typically containing a single gene tree).
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
GNU Scientific, GNU Multiple Precision Arithmetic, GNU MPFR, SQLite3
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Diego Mallo

Publication for SimPhy

SimPhy citations

 (8)
library_books

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

2018
Genes
PMCID: 5867853
PMID: 29495636
DOI: 10.3390/genes9030132

[…] species tree has two polytomies, each with three children, in addition to a short branch (P0) of length 0.2 coalescent units. The S12B tree has a polytomy with five children. For both S12A and S12b, Simphy [] is used to simulate 50 replicates, each with 1000 gene trees. After generating the true gene trees, we used Indelible [] and the general time-reversible model with Gamma rates-across-sites ( […]

library_books

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

2017
PLoS One
PMCID: 5553649
PMID: 28800608
DOI: 10.1371/journal.pone.0182238

[…] ct clock are violated. Many methods are proved consistent and tested empirically only under the strict clock assumption, a situation that we hope our results will change. New simulation tools such as SimPhy make it easy to simulate datasets that deviate from the strict clock assumption.A surprising result of our simulation studies was that while gene tree rooting error was generally high, we could […]

call_split

Anchoring quartet based phylogenetic distances and applications to species tree reconstruction

2016
BMC Genomics
PMCID: 5123309
DOI: 10.1186/s12864-016-3098-z
call_split See protocol

[…] ian dataset [], and datasets used for evaluating ASTRAL-II []. The first two datasets are based on biological data and have a single species tree topology, whereas the last dataset is simulated using SimPhy [] and has a different species tree per replicate and has heterogeneous parameters. Avian and mammalian datasets enable us to evaluate performance for relatively small numbers of species, varyi […]

library_books

Fast Coalescent Based Computation of Local Branch Support from Quartet Frequencies

2016
Mol Biol Evol
PMCID: 4915361
PMID: 27189547
DOI: 10.1093/molbev/msw079

[…] The 201-taxon datasets (200 ingroups plus an outgroup, treated like other taxa here) are simulated using SimPhy (), and has three levels of ILS (), with true discordance that ranges from very low to very high (supplementary fig. S1, Supplementary Material online). Each replicate of the simulation has its […]

library_books

A comparative study of SVDquartets and other coalescent based species tree estimation methods

2015
BMC Genomics
PMCID: 4602346
PMID: 26449249
DOI: 10.1186/1471-2164-16-S10-S2

[…] o new model conditions to this dataset (M1 and M3). In total, our collection has 200 replicate species trees generated under four model conditions (M1, M2, M3, and M4). These data were simulated with SimPhy [] using parameters given in [] and scripts that are available in our github repository. The species trees were simulated using the Yule process, with the birth rate set to 0.000001 per generat […]

library_books

ASTRID: Accurate Species TRees from Internode Distances

2015
BMC Genomics
PMCID: 4602181
PMID: 26449326
DOI: 10.1186/1471-2164-16-S10-S3

[…] These data were presented in [], and provided a variety of model conditions with varying ILS levels, tree shapes, numbers of taxa, and sequence lengths per locus. SimPhy [] was used to generate the species and gene trees, based on two parameters: the number of generations (given as the first number in the model) and the speciation rate (given as the second numb […]

Citations

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SimPhy institution(s)
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain

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