For nucleotide models: Is the lnL score that GARLI reports at the end of a run comparable to the lnL scores reported by other ML search programs?

In general, you should not assume that lnL scores output by other ML search programs (such as PHYML and RAxML) are directly comparable to those output by GARLI, even if they apparently use the same model. To truly know which program has found a better tree you will need to score and optimize the resulting trees using a single program, under the same model. Because of the way that optimization is done in the various programs, PHYML, RAxML and PAUP* are all probably better suited for this final optimization and scoring of a fixed tree than GARLI is.

Also see the previous question. More.

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