What is the upper limit of the Aligner?
One million sequences is the upper limit of the Aligner offered from RDP Fungene website. However, you will not be limited by this number if you can run the command-line version of the Aligner (INFERNAL for rRNA genes, HMMER for protein sequences) from your own computers. Gene models offered by RDP for making alignments can be found at RDP Aligners.
Is there a SOAP version of Aligner?
No, there is not a version of it right now.
Is there a way to include user specified genes in the Aligner?
For making the alignment using RDP Fungene website, the HMM has to be built by RDP Staff ahead of time. If you need to align sequences of genes that are not in the Fungene repository, we welcome you to submit the reference protein sequences (seed sequences) for building HMM alignment models.
The aligner outputs a .tgz file and I am unsure how to open it.
Use 7Zip to unpack any .tgz files. Each .tgz file contains a file to use in the next step of the pipeline. Do not input a .tgz file into the aligner.
How can I run HMMER to align sequences from my computer?
You need to first install HMMER following the installation directions from HMMER Manual. For using HMMER to align sequences, please use 'hmmalign ' command. You can type 'hmmalign -h' to see input/output options. You might need to split the query file into multiple ones if it contains too many sequences. If so, you can merge the separate alignment files using 'AlignmentTools.jar' tool with 'alignment-merger' command from RDPTools package.