Question: What "column weight" really means in RaXML?
0
gravatar for dago
4.6 years ago by
dago2.5k
Germany
dago2.5k wrote:

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?


 

raxml alignment phylogenetics • 1.5k views
ADD COMMENTlink modified 4.3 years ago by saladi130 • written 4.6 years ago by dago2.5k

This question is so specific that you would probably gain more from posting it to the RAxML user group.

ADD REPLYlink written 4.6 years ago by 5heikki8.6k

Thanks, I will follow your advice!

ADD REPLYlink written 4.6 years ago by dago2.5k
0
gravatar for saladi1
4.3 years ago by
saladi130
United States
saladi130 wrote:

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

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by saladi130
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