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 BGIOSGA019217 (Oryza sativa Indica Group)		AlignView depth	PhyloView depth
Eukaryota	~10 Mya	114 species
Viridiplantae	~10 Mya	99 species
Embryophyta	~10 Mya	95 species
Tracheophyta	~10 Mya	93 species
Magnoliophyta	~10 Mya	91 species	202 homologs (oldest homol.)
Mesangiospermae	~10 Mya	89 species	200 homologs
Petrosaviidae	~10 Mya	45 species	63 homologs
commelinids	~10 Mya	43 species	61 homologs
Poaceae	~10 Mya	41 species	60 homologs
BOP_clade	~10 Mya	35 species	54 homologs
Oryzinae	~10 Mya	21 species	31 homologs
Oryza	~10 Mya	19 species	30 homologs (dupl. node) 18 homologs
NAME_4	~10 Mya	17 species	17 homologs
NAME_5	~10 Mya	15 species	15 homologs
NAME_6	~10 Mya	11 species	11 homologs
Oryza_sativa	~10 Mya	7 species	7 homologs
NAME_8	~10 Mya	3 species	3 homologs
Oryza sativa Indica Group	~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