Obtain transfer function from signal flow graph I have a pretty complex signal flow graph with all the blocks and the branches completely describing an analog filter, in the Laplace complex variable s. The signal $X(s)$ is the input and $Y(s)$ is the output.

Is there any (free) tool which can analyze such a graph and provide the overall transfer function $H(s) = Y(s)/X(s)$?

Googling I found this Matlab tool, but the tool it is not free; anyway is there anything similar, in Matlab or in other environments?
I am afraid that for complex systems finding such free standalone tool would be hard. Obviously since you mentioned MATLAB, you should use Simulink then or this tool:

Fully Automated Flowgraph Analysis Tool. Manual to be found here. 

Alternatively you might look into this Mason.m tool. Or this masonry tool.

I know that these guys also did similar work once.