@Hamid Sami Does weka have any license limitations ? I have about 40k features and RapidMiner gives message that it cannot use than more than 1GB RAM in free license.
Border pairs method and bipropagation are two my new very powerful algorithms. Much better than backpropagation. If something is unclear I will explain with pleasure. Please cite me.
You can certainly use WEKA Machine Learning tool for not only classification using classifiers like NN, LIBLINEAR, SVM, Naive Bayes and many others but also one can use it for clustering using different clustering methods, feature dimension reduction using different techniques like PCA, filtering and lots more. It is based on JAVA so you can use across different OS. You can download it for free and see their work in the following link:
http://www.cs.waikato.ac.nz/ml/weka/
Apart form Weka you can use Matlab for NN, SVM etc. But Weka has much more collection.