Root species for Dse (MGP_CAROLIEiJ_G0015232) (Ryukyu mouse) | AlignView depth | PhyloView depth | |
---|---|---|---|
Fungi/Metazoa group | ~1500 Mya | 350 species | |
Bilateria | ~580 Mya | 348 species | |
Chordata | ~550 Mya | 344 species | 705 homologs (oldest homol.) |
Vertebrata | ~550 Mya | 340 species | 701 homologs (dupl. node) 359 homologs |
Euteleostomi | ~420 Mya | 336 species | 355 homologs |
Sarcopterygii | ~400 Mya | 240 species | 254 homologs |
Tetrapoda | ~359 Mya | 238 species | 252 homologs |
Amniota | ~326 Mya | 236 species | 250 homologs |
Mammalia | ~184 Mya | 168 species | 172 homologs |
Theria | ~166 Mya | 166 species | 170 homologs |
Eutheria | ~102 Mya | 158 species | 162 homologs |
Boreoeutheria | ~95 Mya | 149 species | 153 homologs |
Euarchontoglires | ~90 Mya | 104 species | 108 homologs |
Glires | ~81 Mya | 57 species | 57 homologs |
Rodentia | ~80 Mya | 53 species | 53 homologs |
Sciurognathi | ~79 Mya | 39 species | 39 homologs |
Myomorpha | ~51 Mya | 28 species | 28 homologs |
Muroidea | ~44 Mya | 26 species | 26 homologs |
Muridae | ~29 Mya | 24 species | 24 homologs |
Murinae | ~20 Mya | 11 species | 11 homologs |
Mus | ~7 Mya | 9 species | 9 homologs |
Mus_A | ~6 Mya | 7 species | 7 homologs |
Ryukyu mouse | ~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'