For general use, I would like to recommend Hudson's ms, which is definitely the most popular one of all. This masterpiece is also very efficient, qualified for most practical uses. MaCS seems also a competent candidate, but maybe more publications are needed to justify its practical performance.

I have used the following softwares or carefully read their publications and documentations:

  1. ms, by Hudson.
    • Type: standard coalescent-with-recombination; backward in time; continuous time
    • Features: allows for simulating various events such as variable population size, recombination, gene conversion, migration and admixture.
    • Limitations: no selection; no hotspots.
    • Website: Hudson's homepage.
    • Example (from PMID: 16895447):
  2. msHOT, by Hellenthal and Stephens.
    • Type: the same as ms
    • Features: hotspots. msHOT is a modified version of ms.
    • Website: Hudson's homepage.
  3. MaCS, by Chen, Marjoram and Wall
    • Type: Improved SMC
    • Features: much faster than ms while getting similar results to ms. Support complex demographic models including variable population sizes, admixtures and recombination hotspots.
    • Notes: I have briefly tried MaCS. It is lightening fast. For the moment, I do not know whether MaCS delivers similar results to ms on structured populations.
    • Website: Chen's homepage.
    • Example (equivalent to the ms example above):
  4. FastCoal, by Marjoram and Wall.
    • Type: SMC and SMC', approximation to the standard coalescent; move along the sequence; continuous time
    • Features: much faster than ms for large-scale simulation
    • Limitations: constant population size or exponential growth only. To some extent, MaCS is an updated version of FastCoal. If you want to simulate large data set, try MaCS.
    • Website: Marjoram's homepage. (offline since 20080212)
  5. cosi, by Schaffner et al. at the Broad Institute
    • Type: the same as ms
    • Features: variable recombination rate to fit observed data (LD, allele frequency and so on).
    • Website: Schaffner's homepage

I know the following software from other people or from this email:

  1. CoaSim, by Mailund et al. at BIRC, Aarhus University
    • Type: probably the same as ms
    • Features: finite-site mutation; easy post-processing
    • Website: Mailund homepage.
  2. SIMCOAL2, by Laval and Excoffier at the University of Bern
    • Type: Wright-Fisher; discrete-time; backward in time
    • Features: "based on a slower discrete-generation coalescent approach"
    • Website: SIMCOAL2 website.
  3. GENOME, by Liang et al.
    • Type: approximation to the standard coalescent (see below); backward in time; discrete time
    • Approximation: The following sentence indicate the difference between GENOME and ms: "In the standard approach, each coalescent event involves exactly two sequences that coalesce to a common ancestor but, using our approach, multiple sequences can coalesce to a common ancestor simutaneously". I am not sure how this may affect the accuracy of simulation, but the comparison between ms and GENOME seems to be satisfactory.
    • Features: variable population size, recombination and symmetric migration. Claim to be fast.
    • Notes: My experience is GENOME is not as fast as MaCS, although the performance is highly related to the heuristic parameters in use. In addition, this software requires recombinations to happen between segments which may affect the accuracy of very ancient recombinations.
    • Website: Liang's homepage.
  4. FREGENE, by Hoggart et al.
    • Type: apparently the standard coalescent-with-recombination, not sure; forward in time
    • Features: gene conversion and hotspots.
    • Website: FREGENE website at BARGEN
  5. SFS_CODE, by Ryan
    • Type: apparently standard coalescent-with-recombination; forward in time
    • Features: from its website: "SFS_CODE performs forward population genetic simulations under a general Wright-Fisher island model with arbitrary demographic, selective, and mutational effects".
    • Website: SFS_CODE website at SourceForge
  6. Molpopgen, by Thornton
  7. FPG, by Hey et al.
    • Features: forward in time; "useful for assessing the impact of natural selection on genetic variations"
    • Website: Hey's lab page.
  8. SIMCOAL, by Excoffier et al.
  9. EasyPop
  10. simuPOP
  11. BottleSim, by Kuo
  12. TREEVOLVE, by Grassly and Rambaut
  13. Serial SIMCOAL, by Anderson et al.
    • Features: an improved SIMCOAL
    • Website: Hadly Lab