Partitions question ExaBayes 1.4.1

[Pablo Aguado]

Hello everyone,

I have a question regarding partitions. I have 8 partitions with many different loci in them. As an example:

DNA, p56_Depurado_p286_Depurado = 30340-30722, 151538-152135
DNA, p79_Depurado_p116_Depurado_p187_Depurado_p238_Depurado_p269_Depurado_p278_Depurado_p288_Depurado_p362_Depurado = 42154-42542, 61228-61515, 99519-99870, 127348-128357, 143391-143772, 147910-148305, 152666-153147, 190817-191335

When I run ExaBayes it prints:

The program was called as follows:
./yggdrasil -f concatenated.phy -m DNA -q partitions.part -n ConParticiones -s 12345 -c configFile-all-options.nex -T 19

================================================================
You provided an alignment file in phylip format. Trying to parse it...

The (binary) alignment file you provided, consists of the following
partitions:

number: 6
name: p56_Depurado_p286_Depurado
#patterns: 160
type: DNA

number: 7
name: p79_Depurado_p116_Depurado_p187_Depurado_p238_Depurado_p269_Depurado_p278_Depurado_p288_Depurado_p362_Depurado
#patterns: 379
type: DNA

I don't understand the "#patterns:" point. It should be the sum of all pb, right? Its should be much more than 160 or 379, my matrix has 150k pb.

I would be grateful is somebody explained. Thank you in advance,

P.Aguado-Ramsay

[Alexandros Stamatakis]

In all likelihood based tools (BI or ML), identical sites that are
evolving under the same model are typically compressed into patterns to
save on computations, for instance, if your partition has two sites
AAAGGG and AAAGGG they will be compressed into one site pattern that has
a weight of 2, since they will have the same per-site log likelihood.

Alexis

On 16.03.23 11:25, Pablo Aguado wrote:
> Hello everyone,
>
> I have a question regarding partitions. I have 8 partitions with many
> different loci in them. As an example:

> /DNA, p56_Depurado_p286_Depurado = 30340-30722, 151538-152135
> DNA,
> p79_Depurado_p116_Depurado_p187_Depurado_p238_Depurado_p269_Depurado_p278_Depurado_p288_Depurado_p362_Depurado = 42154-42542, 61228-61515, 99519-99870, 127348-128357, 143391-143772, 147910-148305, 152666-153147, 190817-191335/

>
> When I run ExaBayes it prints:

> /The program was called as follows:

> ./yggdrasil -f concatenated.phy -m DNA -q partitions.part -n
> ConParticiones -s 12345 -c configFile-all-options.nex -T 19
>
> ================================================================
> You provided an alignment file in phylip format. Trying to parse it...
>
> The (binary) alignment file you provided, consists of the following

> partitions:/
> /number:6

> name:p56_Depurado_p286_Depurado
> #patterns:160
> type:DNA
>
> number:7
> name:p79_Depurado_p116_Depurado_p187_Depurado_p238_Depurado_p269_Depurado_p278_Depurado_p288_Depurado_p362_Depurado
> #patterns:379

> type:DNA/
> /
> /
> //

> I don't understand the "#patterns:" point. It should be the sum of all
> pb, right? Its should be much more than 160 or 379, my matrix has 150k pb.
>
> I would be grateful is somebody explained. Thank you in advance,
> P.Aguado-Ramsay

> /
> /
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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Pablo Aguado]

Thank you very much for your reply Alexis, understood.

Warm regards,

P.Aguado-Ramsay

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