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:

1. primate subset only
2. placental mammal subset only
3. all 46 vertebrates

Thus, there are six different phylogenetic trees.