Partition for RAxML
Hi,
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.
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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...