Creating phylogenetic trees for a full genome at once?

Question

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Hi,

I have a genome with a thousand genes or so. I’d like to build a maximum likelihood tree for each gene (meaning I’d like to blast each gene against the NCBI NR and take all good homologs then construct a tree for each of the genes).

There used to be a program for this called Phylogenie - but that was a long time ago and it was based on now obsolete programs like formatdb . I wonder if there is any new program that does this?

Any help would be greatly appreciated