bioinformatics - Finding and Comparing Homologous Genes

If you don't have any idea where your gene will have a match with other genes, try something like Blast at the NCBI website.

This will give you a list of hits that you can then use to align with a multiple sequence aligner (MSA). The same NCBI page can give you a tree reconstructed from the results of the searching process, although there is a variety of methods that can be used if you just download the sequences and attempt to build the gene family alignment yourself using "[x] Select All -- Get selected sequences" in the NCBI blast results page, then downloading them in FASTA or other format with "Send to -- File -- Format FASTA -- Create File".

If what you want instead is to include your gene sequence into the best aligning place in an existing gene family alignment, you can try PAGAN.