#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB	gene_extract.hlp
SUB	gene_species_mark.hlp
SUB	organisms.hlp
SUB	gene_species_field_transfer.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		What are Gene-species?

DESCRIPTION	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'.

                You can do that using LINK{gene_extract.hlp}.

		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 LINK{concatenate.hlp})
                and calculate a tree using that alignment.

                You may relink trees based on gene-species to the original organisms
                using LINK{tree_pseudo.hlp}.

NOTES		It's possible to export these gene-species to a separate ARB
                database using the merge tool.

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known