Thanks for replying, ok, i will try what you have suggested. Can you suggest me some paper in which a similar strategy has been followed? The closest that i could find was this: http://www.biomedcentral.com/1471-2164/12/430/figure/F4 in which i think the authors are just showing the presence and absence of genes on a tree made from some other data.
Phylogenetic species tree construction based on presence and absence of a few genes
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Yes it is possible. One simple way is constructing a character matrix for presence / absence of genes and performing a parsimony analysis.
It is correct (at least under certain assumptions), but may prove difficult. First, your genes should be well behaved, that is, genes without a lot of horizontal transmission. Second, it would be better if you were able to distinguish independent gains / losses and code them as different characters on the matrix.
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