How To Compute Dn/Ds From Pairwise Alignment
I have a set of sequences (human 5'utr region), with which I already did pairwise alignment against chimp and rat whole genome. So I have the output in MAF and SAM format.
Is there any existing tool which can take these pairwise alignment and compute the dn/ds score?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Hg19 Strand Information Of Sam Output.
written by Coryza •
-
Sam To Bam - Loss Of Data Or Just Great Compression?
written by Clare
-
Summarizing Mirna-Seq Data Based On Ucsc Hg19 Alignment Results
written by gundalav
-
Removing Phix Data From Ngs Data For Analysis
written by crivenster
-
Solution To Find Out Read Orientation As Well As Strand To Which Reads Align From Sam File
written by k2bhide
-
Samtools View Of A Sam File Entire Chromosome
written by dfernan
-
Error In Converting Sam To Bam By Samtools
written by Raghav
-
Filtering A Sam File For Quality Scores
written by Varun Gupta
-
Sam To Bam Conversion Reference Fasta File
written by Atom Smasher •
-
Soap Result Converted To Bam Not Working In Samtool
written by Sarwar •
Many very similar questions have been asked already, however your question doesn't make sense biologically. You have 5' UnTranslated Regions. There cannot be synonymous or non-synonymous substitutions in untranslated data!
Therefore I will close it. Please read http://en.wikipedia.org/wiki/Ka/Ks_ratio