I have read a lot of articles on computation of NDVI, EVI, SAVI, etc using MODIS product, however nobody has mentioned which of the 1-32 bands were used to compute these indices.
Therefore for MODIS, Red = band 1 (620 – 670 nm) and NIR = band 2 (841 – 876 nm) can be used for NDVI calculation. Find attached supporting paper for more indices.
This is solved, however, I'm still having challenges with importing and clipping of raster image with shapefile polygon. I have SeaDAS but didtn install MODIS processor under tools. I dont know. I have QGIS too, able to import both raster and shapefile, but yet to get how to clipgrip with the shapefile polygon. ENVI and Erdas Machine were suggested, but they are commercial, so QGIS seems ok, but need help on clipping.
Most of the answers to your question are found in Google. Therefore I suggest you do a Google search before asking questions. In fact there are free online tutorials and videos on how to clip, mask etc. which are basic steps in Image processing and Information extraction. As far as access to softwares are concerned, you can use trial versions of ArcGIS for 2 months. This is a temporary solution. But it is surely helpful. Usually the Institutions which you are affiliated with should have software licenses. Therefore the best way would be to use your Institution's machines. Otherwise as you mentioned the option of Opensource is always there. Personally I've used ERDAS Imagine to clip raster images using shapefiles and it works just fine.