What "column weight" really means in RaXML?
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6.2 years ago
dago ★ 2.7k

I am using RaxML to perform a phylogenetic analysis. I use a concatenated alignment of several hundreds of genes.

I found the partitions in this concatenated alignment using Partitionfinder, and I assigned weight to each column in the alignment using ZORRO.

Now, I have a doubt about the "-a" flag in RaxML.

In the manual I can read the following description for the "-a" flag:

"Specify a column weight file name to assign individual weights to each column of the alignment. Those weights must be integers separated by any type and number of white­spaces within a separate file."

Does this mean that using a position weight tells RaxML that position in the alignment with different scores contribute differently to the phylogeny? Meaning that, low-quality positions will still contribute to phylogenetic reconstruction but will do so at a much lower weight.

So for example all columns in the alignment with score of 9 will contribute to the phylogeny much more that all the columns with 0 or 1.

 

Am I missing something here or I understood it correctly?


 

phylogenetics RaxML alignment • 1.8k views
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This question is so specific that you would probably gain more from posting it to the RAxML user group.

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Thanks, I will follow your advice!

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6.0 years ago
saladi1 ▴ 30

For those looking for the response from the mailing list:

"that is correct, but a weight of 9 essentially means that you are 
replicating that site 9 times in the alignment, 

alexis"

https://groups.google.com/forum/#!topic/raxml/Hfpl1cNKxp8

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