I need to estimate the branch lengths of a given phylogenetic tree (i.e. a species tree) under the LG model.
I am aware that PHYLIP accept user trees, but I do not know any method to calculate a distance matrix with the LG model.
I would use RAxML, Phyml or Paml. The former is the fastest one. These programs allow you to fix the topology (species tree) and optimise only the branch lengths.
Why LG? LG+G would be better
Most phylogenetic programs estimate branch lengths for you. You just need to set it in the settings so that it will print/store the branch length information in the resulting tree. You can view the branch lengths in tree visualization programs such as figtree or extract the values using R
Chan
Try our treerate tool.
http://www.hiv.lanl.gov/content/sequence/TREERATEv2/treerate.html
http://www.hiv.lanl.gov/content/sequence/TREERATEv2/treerate_explanation.html
But as Frederico said above, it might be good to also explore your data with LG plus gamma, or other models. Do you have DNA data too, or just protein?
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