Download by right-clicking on the links below and selecting "Save as".

Use the linux applications gzip and tar to decompress the file packages.

• Documentation contains all of the doc pages found here, along with all of the associated file packages. Download, unzip into a host directory, and use this documentation locally. Start by opening the file "Introduction.html" in your web browser.
• All scripts contains all of the python scripts necessary for running mirscan. It includes:
• mirscanTrainer.py
• mirscanExecute.py
• mirscanModule.py
• score_cut.py
• oneSeq.prototype.py
• twoSeq.prototype.py
• Sample files contains sample files for each of the file formats used by mirscan. These files can be used to conduct tests following installation. It includes:
• oneSeq.round0.train: one organism training/foreground.
• twoSeq.round0.train: two organism training/foreground.
• sample1.round0.fax: one organism background.
• sample2.round0.fax: two organism background.
• oneSeq.round0.matrix: one organism scoring matrix made using oneSeq.rubyEtAl.py.
• twoSeq.round0.matrix: two organism scoring matrix made using twoSeq.rubyEtAl.py.
• oneSeq.round0.scr: one organism foreground scoring results.
• twoSeq.round0.scr: two organism foreground scoring results.
• sample1.round0.scr: one organism background scoring results.
• sample2.round0.scr: two organism background scoring results.
• sample1.round1.fax: one organism background after one round of cutting.
• sample2.round1.fax: two organism background after one round of cutting.
• The scoring criteria used in Ruby et al., Genome Res. 2007.
• oneSeq.rubyEtAl.py: single organism criteria.
• twoSeq.rubyEtAl.py: two ortholog criteria.
• Scoring matrices from Ruby et al., Genome Res., 2007.
• generated using oneSeq.rubyEtAl.py:
• dm2_0.matrix ~ dm2_4.matrix: first ~ fifth-round scoring matrices from Drosophila melanogaster (assembly dm2), indexed from zero.
• dp3_0.matrix ~ dp3_4.matrix: first ~ fifth-round scoring matrices from Drosophila pseudoobscura (assembly dp3), indexed from zero.
• dana805_0.matrix ~ dana805_2.matrix: first ~ third-round scoring matrices from Drosophila ananassae (assembly droAna1), indexed from zero.
• dgri805_0.matrix ~ dgri805_2.matrix: first ~ third-round scoring matrices from Drosophila grimshawi (assembly droGri1), indexed from zero.
• dmoj805_0.matrix ~ dmoj805_2.matrix: first ~ third-round scoring matrices from Drosophila mojavensis (assembly droMoj1), indexed from zero.
• dvir805_0.matrix ~ dvir805_2.matrix: first ~ third-round scoring matrices from Drosophila virilis (assembly droVir1), indexed from zero.
• generated using twoSeq.rubyEtAl.py:
• dm2_dp3_0.matrix ~ dm2_dp3_3.matrix: first ~ fourth-round scoring matrices from Drosophila melanogaster/Drosophila pseudoobscura pairs, indexed from zero.
• dm2_dana805_0.matrix ~ dm2_dana805_3.matrix: first ~ fourth-round scoring matrices from Drosophila melanogaster/Drosophila ananassae pairs, indexed from zero.
• dm2_dgri805_0.matrix ~ dm2_dgri805_3.matrix: first ~ fourth-round scoring matrices from Drosophila melanogaster/Drosophila grimshawi pairs, indexed from zero.
• dm2_dmoj805_0.matrix ~ dm2_dmoj805_3.matrix: first ~ fourth-round scoring matrices from Drosophila melanogaster/Drosophila mojavensis pairs, indexed from zero.
• dm2_dvir805_0.matrix ~ dm2_dvir805_3.matrix: first ~ fourth-round scoring matrices from Drosophila melanogaster/Drosophila virilis pairs, indexed from zero.
• dp3_dana805_0.matrix ~ dp3_dana805_3.matrix: first ~ fourth-round scoring matrices from Drosophila pseudoobscura/Drosophila ananassae pairs, indexed from zero.
• dp3_dgri805_0.matrix ~ dp3_dgri805_3.matrix: first ~ fourth-round scoring matrices from Drosophila pseudoobscura/Drosophila grimshawi pairs, indexed from zero.
• dp3_dmoj805_0.matrix ~ dp3_dmoj805_3.matrix: first ~ fourth-round scoring matrices from Drosophila pseudoobscura/Drosophila mojavensis pairs, indexed from zero.
• dp3_dvir805_0.matrix ~ dp3_dvir805_3.matrix: first ~ fourth-round scoring matrices from Drosophila pseudoobscura/Drosophila virilis pairs, indexed from zero.
• dgri805_dana805_0.matrix ~ dgri805_dana805_3.matrix: first ~ fourth-round scoring matrices from Drosophila grimshawi/Drosophila ananassae pairs, indexed from zero.
• dgri805_dmoj805_0.matrix ~ dgri805_dmoj805_3.matrix: first ~ fourth-round scoring matrices from Drosophila grimshawi/Drosophila mojavensis pairs, indexed from zero.
• dgri805_dvir805_0.matrix ~ dgri805_dvir805_3.matrix: first ~ fourth-round scoring matrices from Drosophila grimshawi/Drosophila virilis pairs, indexed from zero.
• dmoj805_dana805_0.matrix ~ dmoj805_dana805_3.matrix: first ~ fourth-round scoring matrices from Drosophila mojavensis/Drosophila ananassae pairs, indexed from zero.
• dmoj805_dvir805_0.matrix ~ dmoj805_dvir805_3.matrix: first ~ fourth-round scoring matrices from Drosophila mojavensis/Drosophila virilis pairs, indexed from zero.
• dvir805_dana805_0.matrix ~ dvir805_dana805_3.matrix: first ~ fourth-round scoring matrices from Drosophila virilis/Drosophila ananassae pairs, indexed from zero.