SimPhy statistics

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SimPhy specifications


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
GNU Scientific, GNU Multiple Precision Arithmetic, GNU MPFR, SQLite3
Maintained Yes



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  • person_outline Diego Mallo <>

Publication for SimPhy

SimPhy in publications

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 […]

PMCID: 5759368
PMID: 29310567
DOI: 10.1186/s12859-017-2002-4

[…] parameters. parameters not varied in that scheme are in italics, datasets were simulated in three schemes, focusing on different parameters. parameters not varied in that scheme are in italics, simphy [] was used to simulate gene trees from species trees, using a coalescence-based wright-fisher model [, ]. the population size, ne, is constant throughout the tree and proportional […]

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

[…] that were previously published. one of the published datasets, rnasim [], includes only one gene tree and is used here only to evaluate the scalability of rooting methods. the other datasets all use simphy [] to generate gene and species trees under the multi-species coalescent (msc) model [] and heterogeneous parameters. we then used indelible [] to simulate nucleotide sequence evolution […]

PMCID: 5123309
DOI: 10.1186/s12864-016-3098-z

[…] 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, […]

PMCID: 4915361
PMID: 27189547
DOI: 10.1093/molbev/msw079

[…] astral and true species tree here and show the rest in the supplementary material online., 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 […]

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

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