pypi: simuPOP | Projects | Ecosyste.ms: Papers

10.1093/molbev/msab175

Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations
Cited by: 10
Author(s): Drew E Terasaki Hart, Anusha P Bishop, Ian Wang
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-019-2611-1

sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs
Cited by: 18
Author(s): Apostolos Dimitromanolakis, Jingxiong Xu, Agnieszka Król, Laurent Briollais
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1006581

Efficient pedigree recording for fast population genetics simulation
Cited by: 112
Author(s): Jerome Kelleher, Kevin R. Thornton, Jaime Ashander, Peter L. Ralph
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1008867

VolcanoFinder: Genomic scans for adaptive introgression
Cited by: 56
Author(s): Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio, Joachim Hermisson
Software Mentions: 5
Published: over 4 years ago

10.1186/1755-8794-6-S2-S6

BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
Cited by: 33
Author(s): Carrie Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie
Software Mentions: 5
Published: over 11 years ago

10.3390/toxins11110629

Rapid and Differential Evolution of the Venom Composition of a Parasitoid Wasp Depending on the Host Strain
Cited by: 20
Author(s): Fanny Cavigliasso, Hugo Mathé-Hubert, Laurent Kremmer, Christian Rebuf, Jean‐Luc Gatti, Thibaut Malausa, Dominique Colinet, Marylène Poirié
Software Mentions: 5
Published: almost 5 years ago

10.1002/ece3.2825

Developing approaches for linear mixed modeling in landscape genetics through landscape‐directed dispersal simulations
Cited by: 59
Author(s): Jeffrey R. Row, Steven T. Knick, Sara J. Oyler‐McCance, Stephen C. Lougheed, Bradley C. Fedy
Software Mentions: 4
Published: over 7 years ago

10.1186/s12711-020-0530-2

SeqBreed: a python tool to evaluate genomic prediction in complex scenarios
Cited by: 7
Author(s): Miguel Pérez‐Enciso, Lino C. Ramírez-Ayala, Laura M. Zingaretti
Software Mentions: 4
Published: over 4 years ago

10.1111/eva.12407

Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees
Cited by: 27
Author(s): Victoria L. Pritchard, Jaakko Erkinaro, Matthew Kent, Eero Niemelä, Panu Orell, Sigbjørn Lien, Craig R. Primmer
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0241609

Deaf intermarriage has limited effect on the prevalence of recessive deafness and no effect on underlying allelic frequency
Cited by: 5
Author(s): Derek C. Braun, Shaili Jain, Eric J. Epstein, Brian H. Greenwald, Brienna Herold, Margaret Gray
Software Mentions: 3
Published: almost 4 years ago

10.1093/bioinformatics/btx077

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations
Cited by: 17
Author(s): Ramón Dı́az-Uriarte
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-13-132

Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2
Cited by: 12
Author(s): Michele Pinelli, Giovanni Scala, Roberto Amato, Sérgio Cocozza, Gennaro Miele
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2105-11-S12-S10

interPopula: a Python API to access the HapMap Project dataset
Cited by: 0
Author(s): Tiago Antão
Software Mentions: 3
Published: almost 14 years ago

10.1111/eva.12591

Large-scale genetic panmixia in the blue shark (Prionace glauca): A single worldwide population, or a genetic lag-time effect of the “grey zone” of differentiation?
Cited by: 36
Author(s): Diane Bailleul, Alicia Mackenzie, Olivier Sacchi, François Poisson, Nicolas Bierne, Sophie Arnaud‐Haond
Software Mentions: 3
Published: over 6 years ago

10.1002/ece3.7007

Effective number of white shark ( Carcharodon carcharias, Linnaeus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand
Cited by: 6
Author(s): Danielle Davenport, Paul A. Butcher, Sara Andreotti, Conrad A. Matthee, Andrew Jones, Jennifer R. Ovenden
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-017-1380-2

FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations
Cited by: 19
Author(s): Michał Szpak, Massimo Mezzavilla, Qasim Ayub, Yuan Chen, Yali Xue, Chris Tyler‐Smith
Software Mentions: 3
Published: over 6 years ago

10.1093/bioinformatics/bty197

PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships
Cited by: 28
Author(s): Hannah Meyer, Ewan Birney
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-S2-P47

Effect of environmental factors on gene alterations in complex diseases: simulation study using Gene-Environment iNteraction Simulator 2
Cited by: 0
Author(s): S. Abdalla, Yas Al‐Hadeethi, Ε. K. El-Shewy
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-14-309

High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study
Cited by: 24
Author(s): Sean Hoban, Massimo Mezzavilla, Oscar E. Gaggiotti, Andrea Benazzo, Cock van Oosterhout, Giorgio Bertorelle
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-015-0631-z

Clotho: addressing the scalability of forward time population genetic simulation
Cited by: 0
Author(s): Patrick Putnam, Philip A. Wilsey, Ge Zhang
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-15-48

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms
Cited by: 6
Author(s): Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-12-622

Comparison of measures of marker informativeness for ancestry and admixture mapping
Cited by: 65
Author(s): Lili Ding, Howard W. Wiener, Tilahun Abebe, Mekbib Altaye, Rodney C.P. Go, Carolyn M. Kercsmar, G.A. Grabowski, Lisa J. Martin, Gurjit K. Khurana Hershey, Ranajit Chakorborty, Tesfaye M. Baye
Software Mentions: 2
Published: almost 13 years ago

10.1093/bioinformatics/btt712

forqs: forward-in-time simulation of recombination, quantitative traits and selection
Cited by: 39
Author(s): Darren Kessner, John Novembre
Software Mentions: 2
Published: almost 11 years ago

10.1093/ve/vez003

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination
Cited by: 24
Author(s): Abbas Jariani, Christopher Warth, Koen Deforche, Pieter Libin, Alexei J. Drummond, Andrew Rambaut, F. A. Matsen, Kristof Theys
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1005069

Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution
Cited by: 64
Author(s): Jonathan Terhorst, Christian Schlötterer, Yun S. Song
Software Mentions: 2
Published: over 9 years ago

10.1002/ece3.2182

A test for within‐lake niche differentiation in the nine‐spined sticklebacks ( Pungitius pungitius )
Cited by: 1
Author(s): Federico C. F. Calboli, Pär Byström, Juha Merilä
Software Mentions: 2
Published: over 8 years ago

10.1111/eva.12731

Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake,Sistrurus catenatus
Cited by: 31
Author(s): Michael G. Sovic, Anthony C Fries, Scott A. Martin, H. Lisle Gibbs
Software Mentions: 2
Published: over 5 years ago

10.1002/gepi.21865

Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions
Cited by: 8
Author(s): Jason H. Moore, Ryan C. Amos, Jeff Kiralis, Peter C. Andrews
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep25506

Global diversity in the TAS2R38 bitter taste receptor: revisiting a classic evolutionary PROPosal
Cited by: 64
Author(s): Davide Risso, Massimo Mezzavilla, Luca Pagani, Antonietta Robino, Gabriella Morini, Sergio Tofanelli, Maura Carrai, Daniele Campa, Roberto Barale, Fabio Caradonna, Paolo Gasparini, Donata Luiselli, Stephen Wooding, Dennis Drayna
Software Mentions: 2
Published: over 8 years ago

10.1186/s13040-019-0199-7

Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies
Cited by: 26
Author(s): Marc Joiret, Jestinah Mahachie John, Elena S. Gusareva, Kristel Van Steen
Software Mentions: 1
Published: over 5 years ago

10.1155/2012/628204

Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon
Cited by: 33
Author(s): Anti Vasemägi, Jan Nilsson, P. McGinnity, T. Cross, P. T. O’Reilly, B. Glebe, Bo Peng, Paul R. Berg, Craig R. Primmer
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-16-S12-S1

ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis
Cited by: 31
Author(s): Hao Chen, Peng Yang, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng
Software Mentions: 1
Published: almost 9 years ago

10.1002/ece3.3872

The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation
Cited by: 14
Author(s): Aaron A. Comeault
Software Mentions: 1
Published: over 6 years ago

10.1002/ece3.7143

Can effective population size estimates be used to monitor population trends of woodland bats? A case study of Myotis bechsteinii
Cited by: 3
Author(s): P. G. Wright, Henry Schofield, Fiona Mathews
Software Mentions: 1
Published: over 3 years ago

10.1186/s41065-016-0020-2

Negative frequency dependent selection on sympatric mtDNA haplotypes in Drosophila subobscura
Cited by: 7
Author(s): Göran Arnqvist, Zorana Kurbalija Novičić, José A. Castro, Ahmed Sayadi
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.ajhg.2015.03.012

The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection
Cited by: 45
Author(s): Qasim Ayub, Massimo Mezzavilla, Luca Pagani, Marc Haber, Aisha Mohyuddin, Shagufta Khaliq, S. Qasim Mehdi, Chris Tyler‐Smith
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2156-12-32

Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba
Cited by: 51
Author(s): Erica Bortolotto, Ann Bucklin, Massimo Mezzavilla, Lorenzo Zane, Tomaso Patarnello
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2156-9-66

Calculating expected DNA remnants from ancient founding events in human population genetics
Cited by: 0
Author(s): Andrew W. Stacey, Nathan C. Sheffield, Keith A. Crandall
Software Mentions: 1
Published: almost 16 years ago

10.1007/s00439-016-1641-2

Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas
Cited by: 40
Author(s): Sophie Hackinger, Thirsa Kraaijenbrink, Yali Xue, Massimo Mezzavilla, Asan, George van Driem, Mark A. Jobling, Peter de Knijff, Chris Tyler‐Smith, Qasim Ayub
Software Mentions: 1
Published: over 8 years ago

10.1016/j.fsigen.2014.11.005

Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping
Cited by: 10
Author(s): Massimo Mezzavilla, Martin Geppert, Chris Tyler‐Smith, Lutz Roewer, Yali Xue
Software Mentions: 1
Published: over 9 years ago

10.1534/g3.118.200942

pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species
Cited by: 12
Author(s): Laura M. Zingaretti, Amparo Monfort, Miguel Pérez‐Enciso
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-15-175

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations
Cited by: 5
Author(s): Elsa G. Guillot, Murray P. Cox
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-11-442

Forward-time simulation of realistic samples for genome-wide association studies
Cited by: 33
Author(s): Bo Peng, Christopher I. Amos
Software Mentions: 1
Published: about 14 years ago

10.1186/gb-2010-11-10-r103

Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome
Cited by: 24
Author(s): Jie Zheng, Pavel P. Khil, R. Daniel Camerini‐Otero, Teresa M. Przytycka
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pcbi.1002459

Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability
Cited by: 23
Author(s): Yunpeng Wang, Arne B. Gjuvsland, Jon Olav Vik, Nicolas P. Smith, Peter Hunter, Stig W. Omholt
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.0030047

Forward-Time Simulations of Human Populations with Complex Diseases
Cited by: 50
Author(s): Bo Peng, Christopher I. Amos, Marek Kimmel
Software Mentions: 1
Published: over 17 years ago

10.1186/s12859-015-0525-0

SimBA: simulation algorithm to fit extant-population distributions
Cited by: 3
Author(s): Laxmi Parida, Niina Haiminen
Software Mentions: 1
Published: over 9 years ago

10.3390/molecules15074875

Machine Learning Techniques for Single Nucleotide Polymorphism—Disease Classification Models in Schizophrenia
Cited by: 17
Author(s): Vanessa Aguiar‐Pulido, José A. Seoane, Juan R. Rabuñal, Julián Dorado, Alejandro Pazos, Cristian R. Munteanu
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0250690

Population structure drives cultural diversity in finite populations: A hypothesis for localized community patterns on Rapa Nui (Easter Island, Chile)
Cited by: 4
Author(s): Carl P. Lipo, Robert J. DiNapoli, Mark E. Madsen, Terry L. Hunt
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: simuPOP

Papers Mentioning simuPOP 49