Multiple sequence alignments
Here is a multiple sequence alignment. Assume that it is part of a coding sequence, and starts and ends with a full codon.
CCTGTTCCAGCCGCC
GCTATTCCAGACGCA
Based on the “counting” method, what is dn/ds for this alignment? Can anybody help me with this? much appreciated
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lieven.sterck
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ktalaat •
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you will also need the corresponding protein alignment to calculate this.
I usually use
codemlfrom thePAMLpackage to calculate dn/ds but there are several other options as well