Fly dataset

The fly data set is comprised of 20 real fly genomes in variou states of completion, from the nearly-complete Drosophila melanogaster dm3 (chromosome sequences) to the fragmentary D. rhopaloa droRho (34,000 contigs).

These genomes are real and therefore do not have a root genome or a burnin process.

Tree

This is a combination of the phylogeny presented in the modENCODE white paper proposing the sequencing of eight additional fly genomes (genome.gov) courtesy of Artyom Kopp (UC Davis) and the phylogeny used by UCSC for the 15-way inserct alignment. The Kopp tree lacked droSim1 and droSec1 which were added by normalizing the branch lengths between the dm3 branches on the two trees. Extraneous species were trimmed using tree_doctor from PHAST. This tree is provided for progressive aligners that need a guide tree and will be used in the analysis for StatSigMa-w.

                ((droGri2:0.183954, droVir3:0.093575):0.000000, (droMoj3:0.110563, ((((droBip:0.034265, droAna3:0.042476):0.121927, (droKik:0.097564, ((droFic:0.109823, (((dm3:0.023047, (droSim1:0.015485, droSec1:0.015184):0.013850):0.016088, (droYak2:0.026909, droEre2:0.029818):0.008929):0.047596, (droEug:0.102473, (droBia:0.069103, droTak:0.060723):0.015855):0.005098):0.010453):0.008044, (droEle:0.062413, droRho:0.051516):0.015405):0.046129):0.018695):0.078585, (droPer1:0.007065, dp4:0.005900):0.185269):0.068212, droWil1:0.259408):0.097093):0.035250);

Summary Stats

GenomeChrSize (bp)
dm32L23,011,544
2LHet368,872
2R21,146,708
2RHet3,288,761
3L24,543,557
3LHet2,555,491
3R27,905,053
3RHet2,517,507
41,351,857
M19,517
U10,049,037
Uextra29,004,656
X22,422,827
XHet204,112
YHet347,038
Total168,736,537

Files

Readme with notes on the build process to download and create the flies.seq.tar.gz file (not necessary to download, data is contained in downloadFlies.sh below, this link is here for the sake of a paper trail,): createFlies.txt

Script to download and create the correct directory structure: downloadFlies.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/ - at the moment there are no suggested annotations for the fly package.
  • predictions/ - place your .maf files in here.
  • regions/ - regional analysis takes place in here.
  • sequences/

    flies.seq.tar.gz (1011 MB)

    version: 2

    md5sum: ffbd16a9979bf3d233f59b4422de3315

    sha1sum: 14575f2df189ac03c6d56dcb5b9ce14f2bafa7ba

  • truths/ - leave this empty

tree drawn using phyfi