Gaps in alignment (and how does RAxML treat them)

[Seiler]

Hi,

I have a bit of a naive question, however I could not find a satisfying answer. How does RAxML treat gaps in the alignment. I have a concatenated alignment of several genes and in one of the species this gene is absent. Is RAxML treating this gene as missing data for all species, hence discarding the information, or will it use the data for all species and not for the species this gene is absent? 

Thanks a lot for your help,

Regards

Michael

[Alexandros Stamatakis]

Hi michael,

Please also see previous discussions on this subject:

https://groups.google.com/forum/?hl=de&fromgroups#!searchin/raxml/RAxML
$20treat$20gaps

RAxML will only treat the data as missing that is missing, i.e., only
from that gene and that species were the data is actually missing.

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Seiler]

Hi Alexis,

thanks a lot for your answer. Maybe it could have been obvious, but I am happy that RAxML does not discard the whole gene (all information) where the missing gene occurs, but keeps the information for all the other species.

Bests

Michael

[chris...@googlemail.com]

Hi Alexis,
I was under the impression that alignment columns that are sufficiently gappy were discarded/ignored by RAxML. Your answer above seems to indicate that this is not the case, so that for example if only two of N sequences have a base (and they differ, so that the site is informative), and N-2 have a gap, the site is kept even if N is large. Can you confirm or clarify?
Many thanks,
Chris Wymant

[alexandros...@gmail.com]

That's correct,

Alexis

alexis stamatakis

www.exelixis-lab.org

------ Originalnachricht------

Von:

Datum: Mi., 27. Jan. 2016 18:34

An: raxml;

Betreff:[raxml] Re: Gaps in alignment (and how does RAxML treat them)

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[picas...@gmail.com]

I am kind of in the same situation.Can we add question mark ('?') for this missing gene for this specie ?

[Alexandros Stamatakis]

you can add question mark, gap or N (?, -, N) to represent this,
mathematically those symbols will all be treated in the same way,

alexis

On 04.12.2016 20:53, picas...@gmail.com wrote:
> I am kind of in the same situation.Can we add question mark ('?') for
> this missing gene for this specie ?
>
> On Wednesday, January 27, 2016 at 9:09:58 PM UTC+1, Alexis wrote:
>
> That's correct,
>
>
> Alexis
>
>
> alexis stamatakis
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
>
> ------ Originalnachricht------
>
> *Von: *
>
> *Datum: *Mi., 27. Jan. 2016 18:34
>
> *An: *raxml;
>
> *Betreff:*[raxml] Re: Gaps in alignment (and how does RAxML treat them)

> send an email to raxml+un...@googlegroups.com <javascript:>.

> For more options, visit https://groups.google.com/d/optout

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[Wei Chen]

Hello Alexis,

In this case if the gaps are presented as -, I don't need to change anything(like change to mark "?") to refer as they are missing data because they

will be treated in the same way.Is it correct?

                                                                 Wei 

Alexis於 2016年12月5日星期一 UTC+1下午3時56分58秒寫道：

[Alexandros Stamatakis]

that's correct,

alexis

On 19.05.2017 11:38, Wei Chen wrote:
>
>
>
> Hello Alexis,
> In this case if the gaps are presented as -, I don't need to change
> anything(like change to mark "?") to refer as they are missing data
> because they
> will be treated in the same way.Is it correct?
>
> Wei
>
>
> Alexis於 2016年12月5日星期一 UTC+1下午3時56分58秒寫道：
>
> you can add question mark, gap or N (?, -, N) to represent this,
> mathematically those symbols will all be treated in the same way,
>
> alexis
>

> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.

> > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
> --

> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>