[Request] Align unaligned sequences to a profile

[kevinmoran1988]

Would you consider adding an align to profile mode which will insert unaligned sequences into an existing alignment. Basically, akin to mafft's --add or --addfragments mode.

Currently, I can jank this through the profile-profile alignment by passing a single sequence as the second alignment. However, this is cumbersome and adds a layer of complexity.

Also if possible, could you add an option that maintains sequence order? I didn't see any option in help.

Thanks for this wonderful program!

[agudys]

Hello,

Sorry for the late response. Actually, there is no additional complexity underneath when you perform a profile-profile alignment on a profile and unaligned sequence (it was designed to handle such cases). So it is just a matter of command line arguments:

famsa <in_alignment> <sequence> <out_alignment>

or

famsa <in_alignment> -add <sequence> <out_alignment>

Is there any reason why you prefere the latter over the former?

Best,
Adam

[agudys]

Hello @Thernn88
I think I get your point now. You want multiple sequences to be added to the existing alignment. This, indeed, cannot be done directly by FAMSA - repeated profile-profile alignment is the only way. Will think about it!