/pipviewer-0.3.9/README.txt

 1
 2
 3Pip Viewer
 4==========
 5
 6Pipviewer is a visualizer for multiple alignements of genomic
 7sequences.  It highlights conserved regions and allows basic
 8anotations.  Its main goal is to find conserved probes for the
 9construction of gene order data sets.  Selected regions marked as
10'probes' can be expoxted to fasta format.  It can also retreive gene
11annotations form the NBCI and display this information along the
12alignement.
13
14Pipviewer is not an aligner.  You must compute the alignment with
15another tool like Clustal or Multi PIP Maker.  
16
17Pipviewer is a Free Software released under the GNU GPL version 3.
18See `COPYING.txt` for the details.
19
20
21Requirements
22------------
23
24To use this package you will need :
25
26- Python 2.4 or later
27- PyOpenGL 2.0 or later
28- PyQt 3.11 or later
29- vhybridize 0.5.9 or later
30
31
32Installation
33------------
34
35With easy_install:
36
37  easy_install pipviewer
38
39Alternative manual installation:
40
41  tar -zxvf pipviewer-X.Y.Z.tar.gz
42  cd pipviewer-X.Y.Z
43  python setup.py install
44
45Where X.Y.Z is a version number.
46
47If you are not root or if you don't want to install the system
48globally, you should use a
49http://pypi.python.org/pypi/virtualenv[virtualenv].
50
51
52Quick Start
53-----------
54
55Compute a multiple alignment of selected sequences with Multi PIP
56Maker and save the result as `foo.txt`.  Convert the format in a
57representation that pipviewer can use:
58
59  pippacker foo.txt foo.psel
60
61Display the multiple alignment:
62
63  pipviewer foo.psel
64
65You can now select regions by dragging the mouse over them.  Select a
66few regions and mark them as 'probes'.  You can now export those in
67fasta format from the _file_ menu.
68
69If you do not have a multiple alignment handy, you use try pipviewer
70with the files in the `examples` directory.
71
72
73Documentation
74-------------
75
76See the `docs` directory for more documentation.
77
78
79Acknowledgments
80---------------
81
82This original development of this software was done at the
83Comparative Genomics Laboratory at UQAM:
84
85  http://cgl.bioinfo.uqam.ca