Table 1.
Overview of software packages useful for molecular censusing, population structure, and landscape genetics
| Software/method | Usage | Reference | Available from |
|---|---|---|---|
| Mark | Very complete software utilizing maximum likelihood method for capture–mark–recapture studies and more; can accommodate open populations | White and Burnham (1999) | http://welcome.warnercnr.colostate.edu/~gwhite/mark/mark.htm |
| Accumulation curve/rarefaction analysis method | Population-size estimates; does not rely on any specific model | Eggert et al. (2003) | No publicly available software provided |
| Capwire | Maximum likelihood method for capture–mark–recapture studies, can account for two distinct capture probabilities; designed for a single sampling session | Miller et al. (2005) | http://www.webpages.uidaho.edu/~joyce/Lab%20Page/capwire.html |
| Bayesian method for population size estimates | Capture–mark–recapture studies; designed for a single sampling session | Petit and Valiere (2006) | No publicly available software provided |
| Structure | Detects population structure and can assign individuals to populations | Pritchard et al. (2000), Falush et al. (2003) | http://pritch.bsd.uchicago.edu/structure.html |
| Baps | Estimates the number of genetic clusters, detects migrants; accounts for geography | Corander et al. (2003, 2004, 2008) | http://web.abo.fi/fak/mnf//mate/jc/software/baps.html |
| Tess | Detects population structure and migrants; accounts for geography | Francois et al. (2006), Chen et al. (2007) | http://www.timc.imag.fr/Olivier.Francois/tess.html |
| DistLM | Distance-based multivariate regression: useful for analysis of correlates of population structure | McArdle and Anderson (2001) | http://www.stat.auckland.ac.nz/~mja/Programs.htm |
| BIMr | Identifies environmental factors that help explain patterns of geneflow | Faubet and Gaggiotti (2008) | http://www-leca.ujf-grenoble.fr/logiciels.htm |
| Geste | Identifies environmental correlates to genetic structure | Foll and Gaggiotti (2006) | http://www-leca.ujf-grenoble.fr/logiciels.htm |
| Circuitscape | Isolation by resistance approach to studies of genetic structure and gene flow | McRae (2006), McRae and Beier (2007) | http://www.circuitscape.org/Circuitscape/Welcome.html |
Please note that this table is not exhaustive but just an illustration of the methods mentioned in the text. A more detailed overview of computer software for population genetic analysis can be found in Excoffier and Heckel (2006)