GenomicusPlants v41.01

Here you can choose the oldest ancestor of your phylogenetic range of interest and the view you want to display by clicking on one of the following links.

PhyloView will show the conservation of the neighbourhood of the reference gene in the other species, according to the gene phylogenetic tree.
AlignView will align the gene order of the selected species, according to the species phylogenetic tree.

Root species for PHYA (AT1G09570) (Arabidopsis thaliana)		AlignView depth	PhyloView depth
Eukaryota	~10 Mya	114 species
Viridiplantae	~10 Mya	99 species	531 homologs (oldest homol.)
Embryophyta	~10 Mya	95 species	526 homologs (dupl. node) 451 homologs (dupl. node) 441 homologs (dupl. node) 337 homologs (dupl. node) 333 homologs (dupl. node) 260 homologs (dupl. node) 242 homologs
Tracheophyta	~10 Mya	93 species	241 homologs
Magnoliophyta	~10 Mya	91 species	240 homologs (dupl. node) 139 homologs
Mesangiospermae	~10 Mya	89 species	137 homologs
Pentapetalae	~10 Mya	43 species	77 homologs
rosids	~10 Mya	32 species	57 homologs
malvids	~10 Mya	13 species	26 homologs
Brassicaceae	~10 Mya	8 species	19 homologs
Arabidopsis	~10 Mya	3 species	3 homologs
Arabidopsis thaliana	~0 Mya	1 species	1 homolog

Advanced Options

-evalue <Real>
 Expectation value (E) threshold for saving hits
 Default = '10'

-word_size <Integer, >=2>
 Word size for wordfinder algorithm
 Default = '3'

-gapopen <Integer>
 Cost to open a gap
 Default = '11'

-gapextend <Integer>
 Cost to extend a gap
 Default = '1'

-matrix <String>
Scoring matrix name (normally BLOSUM62)

-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
 Default = '11'

-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
 Default = '40'

A more recent version of genomicus is available here