Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Mega:not calculable values for syn/nonsyn substitutions


  • Please log in to reply
No replies to this topic

#1 deha

deha

    member

  • Members
  • Pip
  • 1 posts
0
Neutral

Posted 26 March 2009 - 01:20 AM

Hi,
please, does anyone know why I get not calculable "values" for certain pairwise alignments when calculating synonymous and non-synonymous substitutions? (both when using just number of differences and distances, however the proportion of n/c differs between the models used).
I had this problem if just a single codon was aligned, eg. folowing alignment:
1.GAA
2.GAG
3.GTA
4.AAA
5.GTC
6.GAC

If number of differences was calculated using Nei-Gojobori model, then:
[ 1 2 3 4 5 6 ]
[1]
[2] n/c
[3] n/c n/c
[4] n/c n/c n/c
[5] n/c n/c 1.000 n/c
[6] n/c n/c n/c n/c n/c

I could understand that there is a problem for the pairwise align. where there is more than one substitution between the two codons, but the n/c is present even for single-substitution pairs.

Thanks very much if someone can help.
deha




Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.