"gap" terminology

[Buz Wilson]

This is not an important issue, but I’m giving a talk later this year based on a poy analysis, and I’m curious about what those who work on this program might think.

 

To promote the idea behind direct optimisation, should we be using the words from the fixed alignment terminology “gap” and “gap-extension”? If we are to dispense with the idea of an artificial fixed alignment, should we not call these “indel” and “indel-change”? Or some other term? An alternative is to call it a deletion, when comparing two sequences when one is shorter than the other. Changing “gap” in poy might be difficult (or at least in the “not important” basket), since the program and the documents use this term.

 

George D.F. (Buz) Wilson

Australian Museum (Marine Invertebrates)

6 College Street, Sydney 2010 Australia

tel: +612 9320 6287

fax: +612 9320 6042

email: buz.w...@austmus.gov.au (Museum)

email2: b...@optusnet.com.au (home)

 

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[Paola Pedraza]

Hi there,

To me indel and gap are equivalent terms, and both are inclusive for
insertion and deletion events. I think it is more appropriate to keep
the general and all-inclusive terms in the program to avoid
confusion.... whether gaps represent loss or gain of bases is a post-
analysis assessment.

Paola

On Apr 20, 11:26 pm, "Buz Wilson" <Buz.Wil...@austmus.gov.au> wrote:
> This is not an important issue, but I'm giving a talk later this year
> based on a poy analysis, and I'm curious about what those who work on
> this program might think.
>
> To promote the idea behind direct optimisation, should we be using the
> words from the fixed alignment terminology "gap" and "gap-extension"? If
> we are to dispense with the idea of an artificial fixed alignment,
> should we not call these "indel" and "indel-change"? Or some other term?
> An alternative is to call it a deletion, when comparing two sequences
> when one is shorter than the other. Changing "gap" in poy might be
> difficult (or at least in the "not important" basket), since the program
> and the documents use this term.
>
> George D.F. (Buz) Wilson
>
> Australian Museum (Marine Invertebrates)
>
> 6 College Street, Sydney 2010 Australia
>
> tel: +612 9320 6287
>
> fax: +612 9320 6042
>

> email: buz.wil...@austmus.gov.au (Museum)

[Joe S.]

I think Paola is correct here. Gap insertion costs and extension
costs are widely understood among POY users and others in the
molecular-systematics community as representations of indel events.
Besides being potentially confusing, using alternative terminology in
an effort to promote DI/POY seems more likely to delineate the
position as a strange minority view with its own jargon, resulting in
turning off potential POY users rather than having the intended
effect.

-Joe Spagna