[Bioperl-l] Pipeline for generating phylogenetic trees from list of species names

[saikari keitele]

Hi,

Does anyone know of a simple pipeline for generating a phylogenetic tree
from a list of species with bioperl?
I've had a look at
http://www.bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline#Distance_Distance_in_PHYLIP_.2B_NJ_Tree_in_PHYLIPbut
it isn't explicit for the crucial steps (at least given my level of
knowledge)
For each species, should I extract the longest sequence available for every
protein and align it with the same protein sequences of the other species in
the list?

Would anyone have an example pipeline of the different steps to perform?

Thank you very much.

Saikari