[BiO BB] Ka/Ks

[D. Norris]

  ----- Original Message ----- 
  From: Peter Groenen 
  To: bio_bulletin_board at bioinformatics.org 
  Sent: Friday, June 25, 2004 5:27 PM
  Subject: [BiO BB] Ka/Ks


  I am looking for a command line tool that can handle protein alignments as input and aligns the corresponding transcripts. I want to use it for Ka/Ks determination.
  Secondly, I need something like a "sliding " Ka/Ks determination to see if there is a difference within a protein when looking at smaller segments. 
  I looked at SNAP, and also PAML but they are not very straightforward in use, especially hte diffenret formats are giving me trouble.
  Any ideas?
  Thanks in advance.
  Peter
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