$git clone https://github.com/zhutao1009/dnds.git>>>from dnds import dnds
>>>seq1='CTGTGCACT'
>>>seq2='CTATCCGCT'
>>>dnds_test=dnds(seq1,seq2)
pn=0.315789,ps=0.375000
dn=0.409908,ds=0.519860
dn/ds=0.788496
>>>print (dnds_test)
0.788496 $cat demo.fa
>NP_000006.1_1
ATGGACATTGAAGCATATTTTGAAAGAATTGGCTATAAGAACTCTAGGAACAAATTGGACTTGGAAACATTAACTGACATTCTTGAGCACCAGATCCGGGCTGTTCCCTTTGAGAACCTTAACATGCATTGTGGGCAAGCCATGGAGTTGGGCTTAGAGGCTATTTTTGATCACATTGTAAGAAGAAACCGGGGTGGGTGGTGTCTCCAGGTCAATCAACTTCTGTACTGGGCTCTGACCACAATCGGTTTTCAGACCACAATGTTAGGAGGGTATTTTTACATCCCTCCAGTTAACAAATACAGCACTGGCATGGTTCACCTTCTCCTGCAGGTGACCATTGACGGCAGGAATTACATTGTCGATGCTGGGTCTGGAAGCTCCTCCCAGATGTGGCAGCCTCTAGAATTAATTTCTGGGAAGGATCAGCCTCAGGTGCCTTGCATTTTCTGCTTGACAGAAGAGAGAGGAATCTGGTACCTGGACCAAATCAGGAGAGAGCAGTATATTACAAACAAAGAATTTCTTAATTCTCATCTCCTGCCAAAGAAGAAACACCAAAAAATATACTTATTTACGCTTGAACCTCGAACAATTGAAGATTTTGAGTCTATGAATACATACCTGCAGACGTCTCCAACATCTTCATTTATAACCACATCATTTTGTTCCTTGCAGACCCCAGAAGGGGTTTACTGTTTGGTGGGCTTCATCCTCACCTATAGAAAATTCAATTATAAAGACAATACAGATCTGGTCGAGTTTAAAACTCTCACTGAGGAAGAGGTTGAAGAAGTGCTGAAAAATATATTTAAGATTTCCTTGGGGAGAAATCTCGTGCCCAAACCTGGTGATGGATCCCTTACTATT
>NP_000006.1_2
ATGGACATCGAAGCATACTTTGAAAGGATTGGTTACAAGAACTCAGTGAATAAATTGGACTTAGCCACATTAACTGAAGTTCTTCAGCACCAGATGCGAGCAGTTCCTTTTGAGAATCTTAACATGCATTGTGGAGAAGCCATGCATCTGGATTTACAGGACATTTTTGACCACATAGTAAGGAAGAAGAGAGGTGGATGGTGTCTCCAGGTTAATCATCTGCTGTACTGGGCTCTGACCAAAATGGGCTTTGAAACCACAATGTTGGGAGGATATGTTTACATAACTCCAGTCAGCAAATATAGCAGTGAAATGGTCCACCTTCTAGTACAGGTGACCATCAGTGACAGGAAGTACATTGTGGATTCCGCCTATGGAGGCTCCTACCAGATGTGGGAGCCTCTGGAATTAACATCTGGGAAGGATCAGCCTCAGGTGCCTGCCATCTTCCTTTTGACAGAGGAGAATGGAACCTGGTACTTGGACCAAATCAGAAGAGAGCAGTATGTTCCAAATGAAGAATTTGTTAACTCAGACCTCCTTGAAAAGAACAAATATCGAAAAATCTACTCCTTTACTCTTGAGCCCCGAGTTATCGAGGATTTTGAATATGTGAATAGCTATCTTCAGACATCGCCAGCATCTGTGTTTGTAAGCACATCGTTCTGTTCCTTGCAGACCTCGGAAGGGGTTCACTGTTTAGTGGGCTCCACCTTTACAAGTAGGAGATTCAGCTATAAGGACGATGTAGATCTGGTTGAGTTTAAATATGTGAATGAGGAAGAAATAGAAGATGTACTGAAAACCGCATTTGGCATTTCTTTGGAGAGAAAGTTTGTGCCCAAACATGGTGAACTAGTTTTTACTATT
$python dnds.py demo.fa
pn=0.150498,ps=0.448961
dn=0.167981,ds=0.684625
dn/ds=0.245362 The KaKs_Calculator result:
| Sequence | Method | Ka | Ks | Ka/Ks | P-Value(Fisher) | Length | S-Sites | N-Sites | Fold-Sites(0:2:4) | Substitutions | S-Substitutions | N-Substitutions | Fold-S-Substitutions(0:2:4) | Fold-N-Substitutions(0:2:4) | Divergence-Time | Substitution-Rate-Ratio(rTC:rAG:rTA:rCG:rTG:rCA/rCA) | GC(1:2:3) | ML-Score | AICc | Akaike-Weight | Model |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NP_000006.1 | NG | 0.163702 | 0.684541 | 0.239141 | 1.54E-17 | 870 | 192.31 | 677.69 | NA | 186 | 86.3333 | 99.6667 | NA | NA | 0.278831 | 1:1:1:1:1:1 | 0.422989(0.468966:0.32931:0.47069) | NA | NA | NA | NA |
M Nei, T Gojobori, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions., Molecular Biology and Evolution, Volume 3, Issue 5, September 1986, Pages 418–426, https://doi.org/10.1093/oxfordjournals.molbev.a040410
Warning: this program was tested based on python3