Below I will describe a typical workflow for phylogenetic analysis.

1) Use annotation tree viewer (it is situated under the sequence view) to check details of BLAST feature



2) Select sequences, which you would like to add to alignment, right click on them and then choose "Fetch sequences from remote database". The selected sequences will be downloaded into single Fasta file with name defined by ID (for example accession number).



3) Multifasta file will open automatically after sequences are downloaded. Convert it to multiple alignment format.




4) Align sequences using suitable algorithm.
MUSCLE, KAlign, T-Coffee and Clustal tools are availble.
Then build a phylogenetic tree (using built-in Phylip capabilities).