Расчет Ka/Ks с помощью Pal2Nal

PAL2NAL output Ka/Ks(fasta-format)

>MALK_ECOLI
atggcgagcgtacagctgcaaaatgtaacgaaagcctggggcgaggtcgtggtatcgaaa
gatatcaatctcgatatccatgaaggtgaattcgtggtgtttgtcggaccgtctggctgc
ggtaaatcgactttactgcgcatgattgccgggcttgagacgatcaccagcggcgacctg
ttcatcggtgagaaacggatgaatgacactccgccagcagaacgcggcgttggtatggtg
tttcagtcttacgcgctctatccccacctgtcagtagcagaaaacatgtcatttggcctg
aaactggctggcgcaaaaaaagaggtgattaaccaacgcgttaaccaggtggcggaagtg
ctacaactggcgcatttgctggatcgcaaaccgaaagcgctctccggtggtcagcgtcag
cgtgtggcgattggccgtacgctggtggccgagccaagcgtatttttgctcgatgaaccg
ctctccaacctcgatgctgcactgcgtgtgcaaatgcgtatcgaaatctcccgtctgcat
aaacgcctgggccgcacaatgatttacgtcacccacgatcaggtcgaagcgatgacgctg
gccgacaaaatcgtggtgctggacgccggtcgcgtggcgcaggttgggaaaccgctggag
ctgtaccactatccggcagaccgttttgtcgccggatttatcggttcgccaaagatgaac
ttcctgccggtaaaagtgaccgccaccgcaatcgatcaagtgcaggtggagctgccaaat
cgtcagcaagtctggctgccagttgaaagccgtgatgtccaggttggagccaatatgtcg
ctgggtattcgcccggaacatctactgccgagtgatatcgctgacgtcatccttgagggt
gaagttcaggtcgtcgagcaactcggcaacgaaactcaaatccatatccagatcccttcc
attcgtcaaaacctggtgtaccgccagaacgacgtggtgttggtagaagaaggtgccaca
ttcgctatcggcctgccgccagagcgttgccatctgttccgtgaggatggcactgcatgt
cgtcgactgcataaggagccgggcgtt
>choler
atggcgagtgtcacgttaaaaaatgtatgtaaagcttatggcgatgtgctgatttccaag
aatgtcgacctagagattcaagaaggcgaattcgtggtattcgtaggtccttcaggttgt
ggtaaatccactctactgcgctgtatcgcaggtttagaggacattacgtctggcgacctg
ttcatcggtgagcagcgcatgaatgatgtggaaccgtccaaacgcggtgtcggtatggtt
ttccagtcttacgcgctttacccgcacctcaatttgtacgacaacatgtcatttggcctt
aagctctccaaagccgataaaagcgagatcaaaaaacgcgttgaccatgcggcggaaatt
ctgcaactgagccacctgctcgatcgtcaacccaaagcgctttctggcggtcaacgccag
cgtgtagccattggccgtactctggtttcacagcccaacgtattcctgctggatgaaccg
ctatccaacctcgatgccgctttgcgcgtgcaaatgcgttcagaaattaccaaactgcaa
cgtaaactgggctgcaccatgatttacgttacccatgaccaagtggaagccatgaccatg
gcggacaaaattgtggtgttggatgcgggttttgtctcgcaagttggcaagccgctggag
ctgtaccactacccacaaaaccgctttgtggccgggtttattggctcgccgaaaatgaac
ttcatgagcgtcttcattgaaggggtagaaaaagatcgggtacaggtccagctttctaac
ggtacgaccttctggatccctgtcgatggcaccactgtcactcgtggagaacgcatgtca
ctcggcattcgtcctgaacatttggtcgaagcagagcatggcgatgccaaaattgaaggc
aaagtaatgatcgttgagaaactgggtaacgaaacccaagtgtatatgaacctgaagggt
tcagactcagatgtgatctaccgccagccagacacactcgatgtcgaaaccggtgacacg
ctcaccattggtattcccgcacatcgctgccatctattccacagtgatggccgtgcttgc
cgccgtttacataaagaaaaaggcgtt





Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
	KS = 2.5960
	KA = 0.2524
	KA/KS = 0.0972
You can see the parameters used in codeml to calculate these values.
If you use these values, please cite the following peper:
	

    * Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology 11:725-736.

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