Phylogenetic tree wth multi-genes but uneven sample

Question

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Hi,

I would like to make a phylogenetic tree with multi genes.

Let say I have :

• 20 samples with gene 1 that have been aligned.
• 18 samples with gene 2 that have been aligned.

So gene 1 has 2 more species than gene 2

1) Since the 2 genes don't have the same sample; can I still concatenate it ?

2) I heard something about adding the character '?' for missing informations. Can I add this question mark character for the 2 species missing in gene 2 ??