Multivariate statistical testing

I wish to conduct a statistical test comparing between two groups where I have multiple boolean dependent variables, i.e. a vector the size of ~7000 that contains ones and zeros. Looking around I saw that there is an extension of the T-test called Hotelling's T-squared distribution. I also found an implementation of this test for Matlab here - http://www.mathworks.com/matlabcentral/fileexchange/2844. As for analyzing more than two groups, I saw that there is a MANOVA package in Matlab, which is the same as ANOVA only for multivariate analysis. Having said that, I know that both T-test and ANOVA are intended for continuous variables, so I'm not sure how correct it will be to use these options.

So my two questions are: 1. Will it be correct to use these methods and if so, is anyone familiar with these implementations and can recommend? 2. If it is not correct to use these, are there other tests I can use instead, and if so can you please point me to their implementations (in Matlab or Java)?

Thanks much! omer