VirAlign for HFV sequences
Purpose: HFValign takes aligned or unaligned
sequences and gives the alignment of pre-defined regions of an appropriate reference sequence.
If your sequences aren't pre-aligned, this tool can align them via a Hidden Markov Model or MAFFT.
Paste your sequence(s) into the space provided, or browse for your file.
Then you may choose options.
Explanation: Please read the Explanation below before using.
: This program is computationally intensive and may take a while to run. Please don't resubmit your request!
HFValign aligns input sequences to a reference sequences and clips the regions the input touched.
There are five options:
The first option forces your job into background mode.
You will receive an email with a link to the results.
The second option asks the program to align your input sequences in one of two ways:
If you have not checked the 'align' option, the input sequences must be pre-aligned.
HMM-align aligns your sequences
based on our curated alignments HMM model.
You can select an appropriate model for your alignement.
is a multiple-sequence alignment program that can align large sequences.
MAFFT is fast, but rough.
The third option codon-aligns your sequences
based on the reference sequence. A compensating mutation must occur within 5 codons (default)
of an initial frameshift so that the shifted reading frame is left intact.
The fourth option inserts a reference sequence
at the top of your input sequences, before they are aligned and/or clipped.
The fifth option translates your alignment to protein sequence.
HFValign attempts to automatically recognize the format of your input file by using
The results page summarizes the running parameters and information about the input, and gives you
the alignment of the region which the input touched
. From this page you can download the alignment in different formats, or send the resulting alignment to
Aligning large sequences is a computationally intensive procedure.
An input file that is pre-aligned and smaller than 500 Kb is run immediately. If your input file exceeds the limit, or if you checked
the 'Align' option
, your job will be run in batch, and you will receive an email when it has finished.
The email contains link to your results.
Questions or comments? Contact us at