I have just finished adding the "[b]in-group/out-group design[/b]" and "[b]FASTA sets from BLAST[/b]" howto's to the Frequently Asked Questions ([url=http://annotathon.univ-mrs.fr/Metagenes/index.php/Frequently_Asked_Questions]FAQ[/url] in the Help menu above). Table of contents is now:
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    1 Translation, ORFs and coding/non-coding status
    2 INTERPRO: Identifying conserved protein domains
    3 BLAST: Finding sequence homologs
    4 Using BLAST to compile a list of FASTA formatted sequence homologs
    5 A microbial view of the Tree Of Life
    6 Designing sequence ingroups and outgroups for phylogenetic tree inference
          6.1 Strategy for defining ingroups and outgroups
          6.2 List of complete microbial genomes at NCBI
          6.3 Common pitfalls & difficulties in building trees
    7 Phylogeny.fr: Infering phylogenetic trees
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Let me know if this covers most foreseeable questions. Since the FAQ is a Wiki, you're also most welcome to update, upgrade, or extend at will (you will need to create a Wiki account since I have have not yet a shared user authentication between the Annotathon and the Wiki).

Good week end to all,
Pascal