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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Copying/Saving consensus sequence http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1172263912 Message started by Sarah on Feb 23^rd, 2007 at 12:51pm

Title: Copying/Saving consensus sequence
Post by Sarah on Feb 23^rd, 2007 at 12:51pm

I haven't been able to figure out how to copy or save a consensus sequence after it has been generated.

After loading a data set, I choose Data > Additional info > Consensus sequence. The sequence appears beneath the alignment, separated by a bar. I've tried saving with "Consensus sequence" still checked, but only the original sequences are saved, and right-clicking doesn't allow the option of copying to clipboard.

Would love some tips!

Sarah

Title: Re: Copying/Saving consensus sequence
Post by Sarah on Feb 23^rd, 2007 at 3:08pm

I figured it out. I can copy the consensus sequence by right-clicking on a non-consensus sequence (i.e., any sequence in the alignment).

Sarah

Title: Re: Copying/Saving consensus sequence
Post by Sarah on Feb 24^th, 2007 at 3:47pm

I discovered a major caveat. It seems impossible to calculate consensus sequences for subsets of an alignment (data file). Instead, one has to spawn a new data panel with the subset, and then find the consensus. It's then possible to copy and save as described above.

Hope this helps others. I found it a slightly unintuitive interface.

Sarah

Title: Re: Copying/Saving consensus sequence
Post by Sergei on Feb 24^th, 2007 at 8:29pm

Dear Sarah,

You are quite right about this being unintuitive. I suppose this stems from an early decision to focus on filtering by site rather than by sequence in the datapanel.

Cheers,
Sergei