Analyzing trees

Here follows some suggestions what to look for when analyzing a tree by inspection:
-To confirm gene orthologs you can check that no species occur on different locations in the tree at the same time.
-If its difficult to analyse a big tree you can analyze parts of it by rebuilding a tree from the big tree, with only the genes in the specific area of interest.
-When two genes show up very close on the tree they are probably a result of a gene duplication event. Usually the shortest branch is keept and the longest branch is removed.