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?