DOI: 10.1093/bioinformatics/bth264. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history

SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history

10.1093/bioinformatics/bth264

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias. Availability: http://cmpg.unibe.ch/software/simcoal2/ Supplementary information: http://cmpg.unibe.ch/software/simcoal2/

Bibliography

Laval, G., & Excoffier, L. (2004). SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics, 20(15), 2485â2487.

Authors 2

Guillaume Laval (first)
Laurent Excoffier (additional)

References 0 Referenced 204

None

Dates

Type	When
Created	21 years, 3 months ago (May 3, 2004, 8:39 p.m.)
Deposited	2 years, 7 months ago (Jan. 25, 2023, 11:07 a.m.)
Indexed	1 week, 3 days ago (Aug. 19, 2025, 6:57 a.m.)
Issued	21 years, 4 months ago (April 29, 2004)
Published	21 years, 4 months ago (April 29, 2004)
Published Online	21 years, 4 months ago (April 29, 2004)
Published Print	20 years, 10 months ago (Oct. 12, 2004)

Funders 0

None

BibTeX

@article{Laval_2004, title={SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history}, volume={20}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/bth264}, DOI={10.1093/bioinformatics/bth264}, number={15}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Laval, Guillaume and Excoffier, Laurent}, year={2004}, month=apr, pages={2485–2487} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        19
      ]
    ],
    "date-time": "2025-08-19T10:57:48Z",
    "timestamp": 1755601068295
  },
  "reference-count": 0,
  "publisher": "Oxford University Press (OUP)",
  "issue": "15",
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2004,
        10,
        12
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title>\n               <jats:p>Summary: We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias.</jats:p>\n               <jats:p>Availability: \u00a0http://cmpg.unibe.ch/software/simcoal2/</jats:p>\n               <jats:p>Supplementary information: \u00a0http://cmpg.unibe.ch/software/simcoal2/</jats:p>",
  "DOI": "10.1093/bioinformatics/bth264",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2004,
        5,
        4
      ]
    ],
    "date-time": "2004-05-04T00:39:00Z",
    "timestamp": 1083631140000
  },
  "page": "2485-2487",
  "source": "Crossref",
  "is-referenced-by-count": 204,
  "title": "SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history",
  "prefix": "10.1093",
  "volume": "20",
  "author": [
    {
      "given": "Guillaume",
      "family": "Laval",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Baltzerstrasse 6, Bern CH-3012, Switzerland"
        }
      ]
    },
    {
      "given": "Laurent",
      "family": "Excoffier",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Baltzerstrasse 6, Bern CH-3012, Switzerland"
        }
      ]
    }
  ],
  "member": "286",
  "published-online": {
    "date-parts": [
      [
        2004,
        4,
        29
      ]
    ]
  },
  "container-title": "Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://academic.oup.com/bioinformatics/article-pdf/20/15/2485/48906082/bioinformatics_20_15_2485.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "syndication"
    },
    {
      "URL": "https://academic.oup.com/bioinformatics/article-pdf/20/15/2485/48906082/bioinformatics_20_15_2485.pdf",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        1,
        25
      ]
    ],
    "date-time": "2023-01-25T16:07:24Z",
    "timestamp": 1674662844000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://academic.oup.com/bioinformatics/article/20/15/2485/233410"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2004,
        4,
        29
      ]
    ]
  },
  "references-count": 0,
  "journal-issue": {
    "issue": "15",
    "published-print": {
      "date-parts": [
        [
          2004,
          10,
          12
        ]
      ]
    }
  },
  "URL": "http://dx.doi.org/10.1093/bioinformatics/bth264",
  "relation": {},
  "ISSN": [
    "1367-4811",
    "1367-4803"
  ],
  "subject": [],
  "published-other": {
    "date-parts": [
      [
        2004,
        10,
        12
      ]
    ]
  },
  "published": {
    "date-parts": [
      [
        2004,
        4,
        29
      ]
    ]
  }
}