Primate dataset

This simulation is intended to be a relatively simple alignment problem as there has been very little evolution that has taken place between the four lineages.

The root genome consisted of hg18 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

                ((simGorilla:0.008825,(simHuman:0.0067,simChimp:0.006667)sHuman-sChimp:0.00225)sG-sH-sC:0.00968,simOrang:0.018318);

Summary Stats

Genome	Chr	Size (bp)
simChimp	A	53,121,445
	B	85,778,862
	C	35,661,804
	D	10,574,168
	Total	185,136,279
simGorilla	A	53,120,926
	B	85,848,133
	C	35,654,756
	D	10,570,608
	Total	185,194,423
simHuman	A	53,106,993
	B	85,835,872
	C	35,630,306
	D	10,572,275
	Total	185,145,446
simOrang	B	85,903,762
	C	35,683,973
	D	10,564,720
	E	37,692,687
	F	15,493,520
	Total	185,338,662

Files

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

An analysis package has the following directory structure:

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

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

README.txt

annotations/

simPrimates.annots.tar.gz (182 MB)

version: 1

md5sum: 7d337b5e4f7c6eeb8eeeda95c2c21271

sha1sum: 6be1156b635d81a29e63349831e003552c7a8277

simPrimates.annots.gff.tar.gz (162 MB)

Annotations in gff format (optional).

version: 2

md5sum: 9f4230f7c2349bd62abd6457be0a42c0

sha1sum: 095d141536819d9e0e8a55a60194d3252d75df55

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

sequences/

simPrimates.seqs.tar.gz (229 MB)

version: 1

md5sum: d817e8739c10a0ddfcbe37200545b7f9

sha1sum: a41f8d1aeb9b0afd58cb7805cc78f28416fdd72d

truths/ - the true mafs are placed in here
- Alignment to the MRCA, ancestor
  simPrimates.ancestor.maf.gz (143 MB)
  
  aligns: {simHuman, simChimp, sHuman-sChimp, simGorilla, sG-sH-sC, simOrang, ancestor}
```
version: 2
```
```
md5sum: 1e2417d2ae8b4cf2743d5e740b7c5ed3
```
```
sha1sum: fac50cbc86e759a1794208ee6e3f1b7d15e95fe2
```
- Alignment to the Root, root
  simPrimates.burnin.maf.gz (581 MB)
  
  aligns: {simHuman, simChimp, sHuman-sChimp, simGorilla, sG-sH-sC, simOrang, ancestor, root}
```
version: 2
```
```
md5sum: 4fb72a9f14cf016c0d7b906d25e4731f
```
```
sha1sum: 6133a7de6788ed71fd2bfad9fea00fb9a439f163
```
- Alignments to the MRCA and Root, with no paralogous blocks, ancestor.noparalogies, burnin.noparalogies
  simPrimates.noparalogyMafs.maf.gz (472 MB)
  
  aligns: {simHuman, simChimp, sHuman-sChimp, simGorilla, sG-sH-sC, simOrang, ancestor, root}
```
version: 2
```
```
md5sum: 3fc4fcb8fa64958f2a9d655b992387f7
```
```
sha1sum: c8714fd9adb64e27a615f08d35c900529034b2f7
```

tree drawn using phyfi