MADS Domain Protein Phylogeny Reconstructions
The phylogenetic trees linked from this page were constructed from
alignments which were computed as outlined on the
alignment page. All protein sequences
from the genes listed in the MADS box
gene list are included in this analysis. Phylogeny reconstruction
was performed with the
Phylogeny
Inference Package (PHYLIP). Distance matrices were calculated from
the alignments with the protdist program, and these were
used to construct phylogenies by neighbor joining with the
neighbor program. The trees are made available in
the "New Hampshire" source format, which you may use to view the trees
with programs like
treetool
or
treeview.
Additionally, PostScript
graphics are provided, which you can view directly with your web
browser if your browser can display PostScript or it is configured
to use a viewer application, such as ghostview, for this purpose.
As another option, we also provide GIF files which are generated from
the PostScript graphics using
ghostscript.
- MADS domain tree: source,
PostScript tree style or
dendrogram style,
GIF tree style or
dendrogram style.
This tree is constructed on the basis of an
alignment MADS domain sequences
(60 amino acids long). The MADS domain is the only sequence stretch
that is clearly homologous among all MADS domain proteins from
animals, fungi and plants. The tree allows a rough classification of
genes into gene subfamilies.
- MIK domain tree: source,
PostScript tree style or
dendrogram style,
GIF tree style or
dendrogram style.
This tree is computed from an
alignment of the MIK domain
which, in addition to the MADS domain, also comprises the
I region and the K domain, which are only found in plant
MADS domain proteins. The MIK domain is approximately 170
amino acids long, length heterogeneity is particularly found
in the rather variable I region. The phylogenetic tree provides
some interesting hints about the radiation and evolution of
MIK type genes in plants.
