GenomicusPlants v49.01

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	158 species
archaeplastida	148 species
viridiplantae	142 species	853 homologs (oldest homol.)
streptophyta	138 species	848 homologs (dupl. node) 833 homologs (dupl. node) 819 homologs (dupl. node) 256 homologs
embryophyta	136 species	255 homologs
magnoliophyta	133 species	254 homologs
mesangiospermae	131 species	253 homologs
pentapetalae	74 species	139 homologs
rosids	57 species	103 homologs
malvids	20 species	37 homologs
brassicaceae	11 species	26 homologs
arabidopsis	4 species	4 homologs
arabidopsis.thaliana	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'