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/pipviewer-0.3.9/README.txt

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Possible License(s): GPL-3.0
  1. Pip Viewer
  2. ==========
  3. Pipviewer is a visualizer for multiple alignements of genomic
  4. sequences. It highlights conserved regions and allows basic
  5. anotations. Its main goal is to find conserved probes for the
  6. construction of gene order data sets. Selected regions marked as
  7. 'probes' can be expoxted to fasta format. It can also retreive gene
  8. annotations form the NBCI and display this information along the
  9. alignement.
  10. Pipviewer is not an aligner. You must compute the alignment with
  11. another tool like Clustal or Multi PIP Maker.
  12. Pipviewer is a Free Software released under the GNU GPL version 3.
  13. See `COPYING.txt` for the details.
  14. Requirements
  15. ------------
  16. To use this package you will need :
  17. - Python 2.4 or later
  18. - PyOpenGL 2.0 or later
  19. - PyQt 3.11 or later
  20. - vhybridize 0.5.9 or later
  21. Installation
  22. ------------
  23. With easy_install:
  24. easy_install pipviewer
  25. Alternative manual installation:
  26. tar -zxvf pipviewer-X.Y.Z.tar.gz
  27. cd pipviewer-X.Y.Z
  28. python setup.py install
  29. Where X.Y.Z is a version number.
  30. If you are not root or if you don't want to install the system
  31. globally, you should use a
  32. http://pypi.python.org/pypi/virtualenv[virtualenv].
  33. Quick Start
  34. -----------
  35. Compute a multiple alignment of selected sequences with Multi PIP
  36. Maker and save the result as `foo.txt`. Convert the format in a
  37. representation that pipviewer can use:
  38. pippacker foo.txt foo.psel
  39. Display the multiple alignment:
  40. pipviewer foo.psel
  41. You can now select regions by dragging the mouse over them. Select a
  42. few regions and mark them as 'probes'. You can now export those in
  43. fasta format from the _file_ menu.
  44. If you do not have a multiple alignment handy, you use try pipviewer
  45. with the files in the `examples` directory.
  46. Documentation
  47. -------------
  48. See the `docs` directory for more documentation.
  49. Acknowledgments
  50. ---------------
  51. This original development of this software was done at the
  52. Comparative Genomics Laboratory at UQAM:
  53. http://cgl.bioinfo.uqam.ca