Human/hg19/GRCh37 46-way multiple alignment
The 46 species multiple alignment on human/hg19/GRCh37 is an extra large bit of work. A discussion of the phylogenetic trees used in the alignment is included here.
Errata
The initial release of this track include a phylogenetic tree that had two small errors in it.
46way.nh
Namely: Baboon (papHam1) and Rhesus (rheMac2) were specified as separate nodes instead
of correctly sister species. The same problem is present for Wallaby (macEug1) and
Opossum (monDom5). The discussion below includes a corrected phylogenetic tree.
Corrected Tree
I'm currently rerunning a test with the multiple alignment and phastCons/phyloP annotations to see if the corrected tree makes any significant difference in the result. I'm expecting the difference to be minor. In the meantime, included here is a corrected tree:
((((((((((((((((( hg19:0.006690,panTro2:0.006663):0.002736,gorGor1:0.008781):0.009574, ponAbe2:0.018320):0.014347, (rheMac2:0.007863,papHam1:0.007644):0.029610):0.021965, calJac1:0.066248):0.057725,tarSyr1:0.138111):0.011068, (micMur1:0.092694,otoGar1:0.129822):0.035615):0.015654, tupBel1:0.186600):0.004734,(((((mm9:0.084475,rn4:0.091689):0.198456, dipOrd1:0.212120):0.022998,cavPor3:0.225832):0.009965, speTri1:0.148889):0.025869,(oryCun2:0.113952, ochPri2:0.201056):0.101863):0.015314):0.020677, (((vicPac1:0.107300,(turTru1:0.064649,bosTau4:0.123608):0.025219):0.040465, ((equCab2:0.109511,(felCat3:0.098624,canFam2:0.102582):0.050027):0.006078, (myoLuc1:0.142585,pteVam1:0.113375):0.033777):0.004432):0.011563, (eriEur1:0.222118,sorAra1:0.269476):0.056631):0.021325):0.023667, (((loxAfr3:0.082207,proCap1:0.155479):0.026990,echTel1:0.246016):0.049975, (dasNov2:0.116621,choHof1:0.096458):0.053301):0.006623):0.234681, (monDom5:0.126451,macEug1:0.122582):0.215267):0.074190, ornAna1:0.453572):0.105220,((galGal3:0.164727,taeGut1:0.171381):0.198499, anoCar1:0.489779):0.107898):0.188168,xenTro2:0.847575):0.300265, (((tetNig2:0.223507,fr2:0.203488):0.182455, (gasAcu1:0.310214,oryLat2:0.480345):0.073203):0.316470, danRer6:0.731528):0.180826):0.480450,petMar1:0.480450);
Almost in linear format:
((((((((((((((((( hg19 : 0.006690 , panTro2 : 0.006663 ): 0.002736 , gorGor1 : 0.008781 ): 0.009574 , ponAbe2 : 0.018320 ): 0.014347 ,( rheMac2 : 0.007863 , papHam1 : 0.007644 ): 0.029610 ): 0.021965 , calJac1 : 0.066248 ): 0.057725 , tarSyr1 : 0.138111 ): 0.011068 ,( micMur1 : 0.092694 , otoGar1 : 0.129822 ): 0.035615 ): 0.015654 , tupBel1 : 0.186600 ): 0.004734 ,((((( mm9 : 0.084475 , rn4 : 0.091689 ): 0.198456 , dipOrd1 : 0.212120 ): 0.022998 , cavPor3 : 0.225832 ): 0.009965 , speTri1 : 0.148889 ): 0.025869 ,( oryCun2 : 0.113952 , ochPri2 : 0.201056 ): 0.101863 ): 0.015314 ): 0.020677 ,((( vicPac1 : 0.107300 ,( turTru1 : 0.064649 , bosTau4 : 0.123608 ): 0.025219 ): 0.040465 ,(( equCab2 : 0.109511 ,( felCat3 : 0.098624 , canFam2 : 0.102582 ): 0.050027 ): 0.006078 ,( myoLuc1 : 0.142585 , pteVam1 : 0.113375 ): 0.033777 ): 0.004432 ): 0.011563 ,( eriEur1 : 0.222118 , sorAra1 : 0.269476 ): 0.056631 ): 0.021325 ): 0.023667 ,((( loxAfr3 : 0.082207 , proCap1 : 0.155479 ): 0.026990 , echTel1 : 0.246016 ): 0.049975 ,( dasNov2 : 0.116621 , choHof1 : 0.096458 ): 0.053301 ): 0.006623 ): 0.234681 ,( monDom5 : 0.126451 , macEug1 : 0.122582 ): 0.215267 ): 0.074190 , ornAna1 : 0.453572 ): 0.105220 ,(( galGal3 : 0.164727 , taeGut1 : 0.171381 ): 0.198499 , anoCar1 : 0.489779 ): 0.107898 ): 0.188168 , xenTro2 : 0.847575 ): 0.300265 ,((( tetNig2 : 0.223507 , fr2 : 0.203488 ): 0.182455 ,( gasAcu1 : 0.310214 , oryLat2 : 0.480345 ): 0.073203 ): 0.316470 , danRer6 : 0.731528 ): 0.180826 ): 0.480450 , petMar1 : 0.480450 );
Multiple Trees
For the phyloP/phastCons calculations, there are a number of trees that were used.
There is a set of trees with branch lengths calculated based only on the ordinary chromosomes without chrX, and a set of trees calculated based only on chrX.
Within those two categories, there are three trees with branch lengths calculated from subsets of the 46 species:
- primate subset only
- placental mammal subset only
- all 46 vertebrates
Thus, there are six different phylogenetic trees.
