Question: Partition for RAxML
gravatar for fec2
21 months ago by
fec230 wrote:


I would like to construct a phylogenomic tree using core-gene alignment (~1100 protein coding genes) of 24 taxa using RAxML. From the manual I noticed that I need to partition the dataset. Is that mean that I need to prepare txt file that define the partition? So I gene = 1 partition? Is there an easy way to prepare the txt file? Will the result be really affected without the partition? Thank you.

ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 21 months ago by fec230

What format are the aligned core genes in at the moment? Fasta?

The simplest way would be to take each of your 1100 alignments, get the alignment length, and write this in to a partition file. If your alignments are already concatenated this will be trickier...

ADD REPLYlink written 19 months ago by Joe16k
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