Genomicus v24.01 - Gene Search

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
Viridiplantae	~10 Mya	84 species
Embryophyta	~10 Mya	80 species	523 homologs (oldest homol. - dupl. node) 507 homologs
Tracheophyta	~10 Mya	78 species	503 homologs
Magnoliophyta	~10 Mya	76 species	502 homologs (dupl. node) 246 homologs (dupl. node) 129 homologs (dupl. node) 116 homologs
Mesangiospermae	~10 Mya	74 species	114 homologs
Pentapetalae	~10 Mya	42 species	62 homologs
rosids	~10 Mya	36 species	54 homologs
Eurosids	~10 Mya	34 species	52 homologs
Malvidae	~10 Mya	23 species	34 homologs
Malvids	~10 Mya	21 species	32 homologs
Brassicales	~10 Mya	17 species	25 homologs
pre alpha	~10 Mya	15 species	23 homologs
Brassicaceae	~10 Mya	13 species	19 homologs
Camelineae	~10 Mya	5 species	5 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