Re: [DIYbio] Re: genetic destances

On Tue, Feb 17, 2015 at 3:18 PM, Iliana Papantonaki
<iliana.nails@gmail.com> wrote:
> My teacher gave me a paper to use as guide and that says
> "To estimate genetic distances, we selected the best fit model of evolution
> for each data set using JMODELTEST 0.1.1 (Guindon & Gascuel 2003; Posada
> 2008) with the Akaike Information Criterion (AIC; Akaike 1974). We
> calculated intra- and interspecific genetic distances using MEGA 4.0 (Tamura
> et al. 2007) for species that were represented by several individuals.
> To assess the presence of barcoding gap (i.e. the gap between intra- and
> interspecific genetic variation), minimum interspecific distances were
> plotted against maximum intraspecific distances .
> We also calcu-lated variability of each of the seven barcodes as the number
> and percentage of variable characters using MEGA 4.0."
>

Did you search the references given in that text? Do you know about
Google Scholar?

MEGA 4.0 seems outdated, as the authors have released a few more
MEGA[number] papers since then... for example here's MEGA6:
http://mbe.oxfordjournals.org/content/30/12/2725.full

(here's MEGA4)
http://www.researchgate.net/profile/Koichiro_Tamura/publication/6342202_MEGA4_Molecular_Evolutionary_Genetics_Analysis_(MEGA)_software_version_4.0/links/00b7d52e6272878b8d000000.pdf

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