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SAMOVA specifications


Unique identifier OMICS_29415
Alternative name Spatial Analysis of MOlecular VAriance
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A file that contains the geographic coordinates of the sampling localities of populations and an Arlequin input file containing the genetic data sampled in populations.
Input format GEO,ARP
Operating system Windows
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes




No version available


  • person_outline Isabelle Dupanloup

Publication for Spatial Analysis of MOlecular VAriance

SAMOVA citations


DNA barcoding a taxonomically complex hemiparasitic genus reveals deep divergence between ploidy levels but lack of species level resolution

PMCID: 5941139
PMID: 29765588
DOI: 10.1093/aobpla/ply026

[…] Tajima’s D and divergence between ploidy levels (DXY).Genetic divergence among sampling localities was explored with spatial analysis of molecular variance (SAMOVA; ), implemented in SPADS v.1.0 (). Spatial analysis of molecular variance maximizes the proportion of genetic variance due to differences among populations (FCT) for a given number of genetic clusters (K-value). We considered the best […]


Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean

BMC Evol Biol
PMCID: 5896055
PMID: 29642852
DOI: 10.1186/s12862-018-1167-4

[…] e four above mentioned parameters (D, Fs, R2, and rg) were applied to each examined population, the overall dataset, as well as the genetically differentiated geographic groups (as inferred mainly by SAMOVA).Since deviations from neutrality are usually caused by changes in effective population size, we also applied Bayesian Skyline plots (BSP) [] to explore the magnitude of historical demographic […]


Climate Is Not All: Evidence From Phylogeography of Rhodiola fastigiata (Crassulaceae) and Comparison to Its Closest Relatives

Front Plant Sci
PMCID: 5912201
PMID: 29713330
DOI: 10.3389/fpls.2018.00462
call_split See protocol

[…] ed with genetic distance (isolation by distance), we conducted a Mental test on matrices of pair-wise geographic distance and FST using ARLEQUIN v 3.5 () with 1,000 random permutations.We performed a spatial analysis of molecular variance (SAMOVA) with SAMOVA v 1.0 (). This program finds the best K-value (number of geographic groups) by maximizing FCT value between K groups of geographically adjac […]


Global connectivity patterns of the notoriously invasive mussel, Mytilus galloprovincialis Lmk using archived CO1 sequence data

BMC Res Notes
PMCID: 5883410
PMID: 29615118
DOI: 10.1186/s13104-018-3328-3
call_split See protocol

[…] In addition, GPS co-ordinates were also missing so we were unable to carry out some crucial tests commonly used in connectivity studies including isolation by distance (IBD) calculations and SAMOVA (spatial analysis of molecular variance). […]


Phylogeographic structure in three North American tent caterpillar species (Lepidoptera: Lasiocampidae): Malacosoma americana, M. californica, and M. disstria

PMCID: 5863710
PMID: 29576956
DOI: 10.7717/peerj.4479
call_split See protocol

[…] locations were grouped to increase sample sizes, and a modified false discovery rate was applied to correct for multiple tests ().To test for the presence of genetic clusters two methods were used: a spatial analysis of molecular variance (SAMOVA) which identifies the maximum between group variance with the use of additional geographic information (K = 2 to 6; 1,000 iterations; ), and a clustering […]


Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PMCID: 5933341
PMID: 29736340
DOI: 10.7717/peerj.4702
call_split See protocol

[…] g BC vs NBC groups. Additionally, another a priori configuration was tested arranging samples into three groups: BC vs. NBC-1 (FOR and CAU) vs. NBC-2 (CUR and SOU).The same data was also processed in Samova 2.0 software (), which implements an approach to define groups of populations that are maximally differentiated from each other while run AMOVA analysis. The software was set to arrange samples […]


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SAMOVA institution(s)
Dipartimento di Biologia, Università di Ferrara, Ferrara, Italy; Laboratoire de Génétique et Biométrie, Département d’Anthropologie, Université de Genève, Switzerland; Zoological Institute, University of Berne, Switzerland
SAMOVA funding source(s)
Supported by a Swiss NSF grant 31-054059.98.

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