HCValign

This is a beta version! There may be bugs or other problems. Please use with GREAT care and let use know any problems you have. Since this tool is being actively developed, we will fix them quickly.

Purpose: HCValign takes one or more nucleotide sequences in any standard format and aligns them to our sequence Hidden Markov Model. This tool can be used to align your sequences based on our complete DNA alignments.

Usage: Paste your sequence(s) into the space provided, or browse for your file. Then, select a HMM Model, or let program decide.

Explanation: HCValign was developed from a implementation of HMMER package. HCValign attempts to automatically recognize the format of your input file by using Format Conversion.

Aligning large size sequences is a computationally intensive procedure. Currently, input files which is pre-aligned smaller than 500 Kb or which is not pre-aligned smller than 50 Kb for the user selected model are run immediately; if your input file exceeds the limit or uses the model by program decide, your job will be run in batch, and you will receive an email when it has finished. The email contains link to your results.