source: branches/lib/HELP_SOURCE/source/gene_species.hlp

#       main topics:
UP      arb.hlp
UP      glossary.hlp

#       sub topics:
SUB     gene_extract.hlp
SUB     gene_species_mark.hlp
SUB     organisms.hlp
SUB     gene_species_field_transfer.hlp

# format described in ../help.readme


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