Root species for Vapa (ENSRNOG00000014765) (Rat) | AlignView depth | PhyloView depth | |
---|---|---|---|
Fungi/Metazoa group | ~1500 Mya | 399 species | |
Bilateria | ~580 Mya | 397 species | |
Chordata | ~550 Mya | 393 species | 545 homologs (oldest homol.) |
Vertebrata | ~550 Mya | 389 species | 542 homologs |
Gnathostomata | ~473 Mya | 385 species | 539 homologs |
Euteleostomi | ~420 Mya | 383 species | 537 homologs |
Sarcopterygii | ~400 Mya | 253 species | 325 homologs |
Tetrapoda | ~359 Mya | 251 species | 323 homologs |
Amniota | ~326 Mya | 247 species | 319 homologs |
Mammalia | ~184 Mya | 193 species | 262 homologs |
Theria | ~166 Mya | 191 species | 260 homologs |
Eutheria | ~102 Mya | 181 species | 239 homologs |
Boreoeutheria | ~95 Mya | 171 species | 227 homologs |
Euarchontoglires | ~90 Mya | 95 species | 140 homologs |
Euarchontoglires_A | ~90 Mya | 47 species | 56 homologs |
Glires | ~81 Mya | 45 species | 54 homologs |
Rodentia | ~80 Mya | 41 species | 48 homologs |
Rodentia_B | ~80 Mya | 25 species | 30 homologs |
Myomorpha | ~51 Mya | 23 species | 28 homologs |
Muroidea | ~44 Mya | 21 species | 26 homologs |
Muroidea_A | ~44 Mya | 19 species | 24 homologs |
Murinae | ~20 Mya | 11 species | 12 homologs |
Rat | ~0 Mya | 1 species | 2 homologs (dupl. node) 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'