From 02a60145bfa5536eede83dc8fcf5c8921f558b7b Mon Sep 17 00:00:00 2001 From: Guruprasad Anada Date: Tue, 13 Feb 2007 17:01:13 +0000 Subject: [PATCH] --- tools/stats/kaks.xml | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/tools/stats/kaks.xml b/tools/stats/kaks.xml index 0046da41b9f..1cec174f154 100644 --- a/tools/stats/kaks.xml +++ b/tools/stats/kaks.xml @@ -25,6 +25,34 @@ - This tool finds the ratio of the number of nonsynonymous substitutions per nonsynonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks) for the alignments in the input file. +----- + +**Syntax** + +- The input file should contain the aligned sequences in FASTA format + >Seq 1_a + AAAAAAAAAAAGGGGGGGG + >Seq 1_b + AAAAAAGGGGGGGGGGGGG + + + >Seq 2_a + TTTTTTTTTTCCCCCC + >Seq2_b + TTTT-----CCCCCAT + +- The output will have the Ka/Ks value written above each pair of the aligned sequences. + Ka/Ks : 0.14 + >Seq 1_a + AAAAAAAAAAAGGGGGGGG + >Seq 1_b + AAAAAAGGGGGGGGGGGGG + + Ka/Ks : 0.06 + >Seq 2_a + TTTTTTTTTTCCCCCC + >Seq2_b + TTTT-----CCCCCAT