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."
Τη Τετάρτη, 18 Φεβρουαρίου 2015 - 12:47:55 π.μ. UTC+2, ο χρήστης Koeng έγραψε:
-- "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."
Τη Τετάρτη, 18 Φεβρουαρίου 2015 - 12:47:55 π.μ. UTC+2, ο χρήστης Koeng έγραψε:
In what units? Base pairs? nm? Length hypothetically should be pretty easy.Or do you mean sequence differences? Then just blast it.-Koeng
On Tuesday, February 17, 2015 at 2:32:53 PM UTC-8, Iliana Papantonaki wrote:hi all
i need to calculate mean intra- and inter- specific genetic distances for my sequences?
can anyone help me how to do it?
I have 88 sequences/7 species
thankss
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