Serial SimCoal: a population genetics model for data from multiple populations and points in time - PubMed (original) (raw)

Serial SimCoal: a population genetics model for data from multiple populations and points in time

Christian N K Anderson et al. Bioinformatics. 2005.

Abstract

We present Serial SimCoal, a program that models population genetic data from multiple time points, as with ancient DNA data. An extension of SIMCOAL, it also allows simultaneous modeling of complex demographic histories, and migration between multiple populations. Further, we incorporate a statistical package to calculate relevant summary statistics, which, for the first time allows users to investigate the statistical power provided by, conduct hypothesis-testing with, and explore sample size limitations of ancient DNA data.

Availability: Source code and Windows/Mac executables at http://www.stanford.edu/group/hadlylab/ssc.html

Contact: senka@stanford.edu.

PubMed Disclaimer

Similar articles

• HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations.
  Gu S, Pakstis AJ, Kidd KK. Gu S, et al. Bioinformatics. 2005 Oct 15;21(20):3938-9. doi: 10.1093/bioinformatics/bti649. Epub 2005 Aug 30. Bioinformatics. 2005. PMID: 16131520
• GEIGER: investigating evolutionary radiations.
  Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. Harmon LJ, et al. Bioinformatics. 2008 Jan 1;24(1):129-31. doi: 10.1093/bioinformatics/btm538. Epub 2007 Nov 15. Bioinformatics. 2008. PMID: 18006550
• GGtools: analysis of genetics of gene expression in bioconductor.
  Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R. Carey VJ, et al. Bioinformatics. 2007 Feb 15;23(4):522-3. doi: 10.1093/bioinformatics/btl628. Epub 2006 Dec 8. Bioinformatics. 2007. PMID: 17158513 Review.
• VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data.
  Vilella AJ, Blanco-Garcia A, Hutter S, Rozas J. Vilella AJ, et al. Bioinformatics. 2005 Jun 1;21(11):2791-3. doi: 10.1093/bioinformatics/bti403. Epub 2005 Apr 6. Bioinformatics. 2005. PMID: 15814564
• UCSC genome browser: deep support for molecular biomedical research.
  Mangan ME, Williams JM, Lathe SM, Karolchik D, Lathe WC 3rd. Mangan ME, et al. Biotechnol Annu Rev. 2008;14:63-108. doi: 10.1016/S1387-2656(08)00003-3. Biotechnol Annu Rev. 2008. PMID: 18606360 Review.

Cited by

• Opportunities and challenges of macrogenetic studies.
  Leigh DM, van Rees CB, Millette KL, Breed MF, Schmidt C, Bertola LD, Hand BK, Hunter ME, Jensen EL, Kershaw F, Liggins L, Luikart G, Manel S, Mergeay J, Miller JM, Segelbacher G, Hoban S, Paz-Vinas I. Leigh DM, et al. Nat Rev Genet. 2021 Dec;22(12):791-807. doi: 10.1038/s41576-021-00394-0. Epub 2021 Aug 18. Nat Rev Genet. 2021. PMID: 34408318 Review.
• The genetic legacy of legendary and historical Siberian chieftains.
  Zvénigorosky V, Duchesne S, Romanova L, Gérard P, Petit C, Petit M, Alexeev A, Melnichuk O, Gonzalez A, Fausser JL, Solovyev A, Romanov G, Barashkov N, Fedorova S, Ludes B, Crubézy E, Keyser C. Zvénigorosky V, et al. Commun Biol. 2020 Oct 16;3(1):581. doi: 10.1038/s42003-020-01307-3. Commun Biol. 2020. PMID: 33067556 Free PMC article.
• Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.
  Barrera-Redondo J, Piñero D, Eguiarte LE. Barrera-Redondo J, et al. Front Genet. 2020 Jul 15;11:742. doi: 10.3389/fgene.2020.00742. eCollection 2020. Front Genet. 2020. PMID: 32760427 Free PMC article. Review.
• Comparison of Markov Chain Monte Carlo Software for the Evolutionary Analysis of Y-Chromosomal Microsatellite Data.
  Gundlach S, Junge O, Wienbrandt L, Krawczak M, Caliebe A. Gundlach S, et al. Comput Struct Biotechnol J. 2019 Jul 29;17:1082-1090. doi: 10.1016/j.csbj.2019.07.014. eCollection 2019. Comput Struct Biotechnol J. 2019. PMID: 31452861 Free PMC article.
• Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations.
  Silva NM, Rio J, Kreutzer S, Papageorgopoulou C, Currat M. Silva NM, et al. Evol Appl. 2018 Jul 3;11(9):1642-1655. doi: 10.1111/eva.12655. eCollection 2018 Oct. Evol Appl. 2018. PMID: 30344633 Free PMC article.

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.
  • Silverchair Information Systems