In order to work with alignments of genes you first have to extract the wanted genes into some kind of pseudo-species. We called them 'gene-species'.
These gene-species store additional information about the organism and the gene they originated from (in fields 'ARB_origin_gene' and 'ARB_origin_organism'). They only contain that part of the organisms sequence, the gene corresponds to.
The intention is to create different alignments for different groups of genes and to calculate your trees using these alignment(s).
You may also concatenate multiple genes into a multi-gene-alignment (see ´Concatenation of sequences´) and calculate a tree using that alignment.