Thank you @Mensur Dlakic
I have generated a phylogenetic tree using raxml by following command
raxmlHPC -s FcC_supermatrix.phy -n species_tree -M -m GTRGAMMA -f a -x $RANDOM -N 1000 -p 12345 -q FcC_supermatrix_partition.txt
I have obtained a phylogenetic tree with well supported bootstrap value and my final ML Optimization Likelihood value is -45810.705251. Here, I do not know how to interpret the ML optimization Likelihood value. Please, somebody help me to interpret the same. Is it a acceptable value for the given phylogenetic tree?
1 answer
There is no need to interpret the final log likelihood value because it has no meaning on its own. It is more meaningful to look at bootstrap values.
Roughly speaking, the final likelihood is inversely proportional to the size of your alignment (both in terms of length and number of sequences), so I would guess from your likelihood value that you have a relatively short alignment. These values only come into play when you are comparing trees made from the same alignment but with different parameter sets or with different programs. In that case higher likelihood value generally means more reliable tree.
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