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 LIR1 (Os01g0102900) (oryza.sativa)	AlignView depth	PhyloView depth
eukaryota	158 species
archaeplastida	148 species
viridiplantae	142 species
streptophyta	138 species
embryophyta	136 species
magnoliophyta	133 species
mesangiospermae	131 species
commelinids	54 species
poaceae	51 species	62 homologs (oldest homol.)
bop.clade	36 species	36 homologs
oryzinae	15 species	15 homologs (dupl. node) 12 homologs
oryza	13 species	10 homologs
oryza_sativa	5 species	4 homologs
oryza.sativa	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'