Mammal dataset

The mammal dataset contains five species with length evolutionary distances between them. It is the most challenging simulated dataset in the Alignathon

The root genome consisted of hg18 (GRCh36) chr20, chr21 and chr22 with annotations populated from mgcGenes, knownGene, cpgIslandExt and ensGene tracks from the UCSC Table Browser. Details of infile set creation can be gleaned from the evolverInfileGeneration project

The root genome was evolved for a distance of 1.0 via 100 Evolver steps of 0.01, forming the simulation burnin. The final genome of that burnin formed the ancestor for this simulation.

Tree

                ((simCow:0.18908,simDog:0.16303)sCow-sDog:0.032898,(simHuman:0.144018,(simMouse:0.084509,simRat:0.091589)sMouse-sRat:0.271974)sH-sM-sR:0.020593);

Sumamry Stats

Genome	Chr	Size (bp)
simCow	A	42,017,321
	B	86,443,571
	C	33,408,597
	D	6,172,747
	E	24,983,699
	Total	193,025,935
simDog	A	39,124,508
	D	35,271,305
	F	64,906,724
	G	26,567,043
	H	20,782,131
	I	5,551,284
	Total	192,202,995
simHuman	D	15,973,151
	F	41,914,564
	H	2,880,482
	I	13,410,180
	J	88,398,963
	K	28,218,656
	Total	190,795,996
simMouse	A	34,021,255
	F	60,272,644
	L	71,158,916
	M	5,488,388
	N	16,897,397
	O	3,949,899
	P	7,132,917
	Total	198,921,416
simRat	A	45,269,609
	O	4,060,565
	P	7,089,915
	Q	54,146,922
	R	88,137,694
	Total	190,795,996

Files

Script to download and create the correct directory structure: downloadMammals.sh

An analysis package has the following directory structure:

packageMammals/
..  README.txt
..  annotations/
..  predictions/
..  regions/
..  sequences/
..  truths/

These directories may be populated with the following (expand all files):

README.txt

annotations/

simMammals.annots.tar.gz (203 MB)

version: 2

md5sum: bddd7ab44c51b45f79380f190fd7dfa0

sha1sum: 8f672d03b530ca9c3bff2729a50a90dc184aa82a

simMammals.annots.gff.tar.gz (196 MB)

Annotations in gff format (optional).

version: 2

md5sum: db3663a8ea555ffc274b4e7760d6b134

sha1sum: a9a66b6c684afaac5c5560170efa6583856c6ac3

predictions/ - place your .maf files in here.
regions/ - regional analysis takes place in here.

sequences/

simMammals.seqs.tar.gz (303 MB)

version: 1

md5sum: a554a2151b3bbe269c2dcf6e07030ab7

sha1sum: eb7c21e112a8b049c9b69f20522f804a56c5cf01

truths/ - the true mafs are placed in here
- Alignment to the MRCA, ancestor
  simMammals.ancestor.maf.gz (652 MB)
  
  aligns: {simMouse, simRat, sMouse-sRat, simHuman, sH-sM-sR, simCow, simDog, sCow-sDog, ancestor}
```
version: 2
```
```
md5sum: 4bab2832a972a26a9a43af150096295e
```
```
sha1sum: 31395977ecbe948cc0bb4455a5db618e9f543fd2
```
- Alignment to the Root, root
  simMammals.burnin.maf.gz (1.2 GB)
  
  aligns: {simMouse, simRat, sMouse-sRat, simHuman, sH-sM-sR, simCow, simDog, sCow-sDog, ancestor, root}
```
version: 2
```
```
md5sum: 0a4c595644a806e7342ec3be62893f39
```
```
sha1sum: 8bfa54e894a5f276bdfda385e8eeddec90c718bb
```
- Alignments to the MRCA and Root, with no paralogous blocks, ancestor.noparalogies, burnin.noparalogies
  simMammals.noparalogyMafs.maf.gz (1.4 GB)
  
  aligns: {simMouse, simRat, sMouse-sRat, simHuman, sH-sM-sR, simCow, simDog, sCow-sDog, ancestor, root}
```
version: 2
```
```
md5sum: 28fcdd2181ca095b66a73d674d355ae9
```
```
sha1sum: 6dad4195c444ed59c1e0e19857a45266b56561c8
```