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 |
-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'