Yes, there are several software tools available for designing multiplex qPCR assays. These software tools can help researchers design and optimize assays for simultaneous amplification and detection of multiple target sequences in a single reaction. Some commonly used software for multiplex qPCR assay design include:

1. PrimerQuest (Integrated DNA Technologies): PrimerQuest is an online tool provided by Integrated DNA Technologies (IDT). It allows users to design custom qPCR primers and probes for multiplex assays. The tool provides options for primer and probe design, including specifications for multiplexing, melting temperature, and amplicon length.

2. Primer3Plus: Primer3Plus is a web-based tool that supports the design of PCR primers and probes for multiplex qPCR assays. It offers features such as primer and probe design, primer specificity checking, and melting temperature calculations. It also allows users to input multiple target sequences and provides recommendations for multiplex primer sets.

3. AlleleID (Premier Biosoft): AlleleID is a comprehensive software suite for primer and probe design, including multiplex qPCR assays. It offers various algorithms for primer and probe design, specificity checking, and optimization of multiplex reactions. It also provides a visual representation of primer binding sites and target sequences.

4. qBase+ (Biogazelle): qBase+ is a software package designed for qPCR data analysis, but it also includes a module for primer and probe design for multiplex qPCR assays. It offers options for primer design, melting temperature calculations, and probe optimization. It integrates with other qPCR analysis tools, allowing seamless data analysis.

5. Primer-BLAST (NCBI): Primer-BLAST is a web-based tool provided by the National Center for Biotechnology Information (NCBI). It allows users to design primer pairs and probes for multiplex qPCR assays. The tool also performs specificity checking against the NCBI database to avoid potential cross-reactivity with other sequences.

These are just a few examples of software tools available for designing multiplex qPCR assays. It's important to choose a tool based on your specific requirements and experiment setup.

I would like to recommend my project, MultiPrime, which can be found on Github at https://github.com/joybio/multiPrime.

MultiPrime offers a simple and user-friendly approach for generating a list of primers. Users only need to input their sequences of interest, desired product length and some not necessary parameters, and MultiPrime will automatically generate a primer list based on these information.