Using RAxML or ExaML with features instead of dna or porteins

[fhilde]

Hi everyone, I'm quite new to phylogeny but I am trying to construct a tree based on presence absence of certain long terminal repeats. As far as I understood the manual only files that follow the IUPAC code are accepted. While I can easily convert my 0,1 presence, absence matrix into an alignment with only two bases like A and T and format it rightly, I am unsure if this is something RAxML or ExaML can handle well since it's an estimator and maybe not suited for this homogeneous data? Help would be really appreciated.

Cheers Felix

[Pfeiffer, Wayne]

Hi Felix,

Both RAxML8 and RAxML-NG accept binary data with 0s and 1s. For example,

  -m BINGAMMA in RAxML8

and

  --model BIN+G+F in RAxML-NG.

More information for RAxML-NG is at

  https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-sequence-alignment

Good luck!

Wayne

On Aug 20, 2021, at 12:24 AM, fhilde <fhilde...@hotmail.de> wrote:

Hi everyone, I'm quite new to phylogeny but I am trying to construct a tree based on presence absence of certain long terminal repeats. As far as I understood the manual only files that follow the IUPAC code are accepted. While I can easily convert my 0,1 presence, absence matrix into an alignment with only two bases like A and T and format it rightly, I am unsure if this is something RAxML or ExaML can handle well since it's an estimator and maybe not suited for this homogeneous data? Help would be really appreciated.

Cheers Felix

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[Alexey Kozlov]

thank you, Wayne!

On 20.08.21 09:57, Pfeiffer, Wayne wrote:
> Hi Felix,
>
> Both RAxML8 and RAxML-NG accept binary data with 0s and 1s. For example,
>
>   -m BINGAMMA in RAxML8
>
> and
>
>   --model BIN+G+F in RAxML-NG.
>
> More information for RAxML-NG is at
>
> https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-sequence-alignment
> <https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-sequence-alignment>
>
> Good luck!
>
> Wayne
>

>> On Aug 20, 2021, at 12:24 AM, fhilde <fhilde...@hotmail.de <mailto:fhilde...@hotmail.de>> wrote:
>>
>> Hi everyone, I'm quite new to phylogeny but I am trying to construct a tree based on presence
>> absence of certain long terminal repeats. As far as I understood the manual only files that follow
>> the IUPAC

>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__de.wikipedia.org_wiki_IUPAC&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=QDz-wiRlY9zE5rxxvqHCevtBQwPGExdv-9IJhNPslhk&m=N3qXH4YPJsp69fC3ZeM_D0QhkG2Jttm_p3X1BWMk58w&s=Z_TyaENa0XmbgAOMZTVHVJfHENJcuDjA4N5tP9EMUQk&e=>

>> code are accepted. While I can easily convert my 0,1 presence, absence matrix into an alignment
>> with only two bases like A and T and format it rightly, I am unsure if this is something RAxML or
>> ExaML can handle well since it's an estimator and maybe not suited for this homogeneous data? Help
>> would be really appreciated.
>>
>> Cheers Felix
>>
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>> You received this message because you are subscribed to the Google Groups "raxml" group.
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>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_msgid_raxml_0cbbca11-2Df279-2D4cf9-2Db2e1-2D18d6b8b3ce96n-2540googlegroups.com-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dfooter&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=QDz-wiRlY9zE5rxxvqHCevtBQwPGExdv-9IJhNPslhk&m=N3qXH4YPJsp69fC3ZeM_D0QhkG2Jttm_p3X1BWMk58w&s=CUQavOVrMnJQLz2_8uE2eljpZLiqh-ykqcPnhXAA1V0&e=>.

>
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