The GUIDANCE2 Server Server for alignment confidence score
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Select Algorithm GUIDANCE2 GUIDANCE HoT

Warning: GUIDANCE is not suitable for alignments of very few sequences.
As a rule of thumb, use GUIDANCE2 or HoT for less than 8 sequences.

Type your sequences (FASTA format only) * large strings should be uploaded as files

OR
Upload your sequences file (FASTA format only)    

Sequences Type: Amino Acids    Nucleotides   Codons

Select the Input Type     Upload your unaligned (no gaps) sequences file for alignment and evaluation (default) Upload your MSA file for re-alignment and evaluation Upload your MSA file for evaluation only

*This option will evaluate an MSA using the algorithm chosen below. If the uploaded alignment was generated with a different method then the one chosen below, it might affect the results.

Select the MSA algorithm     MAFFT (default) PRANK ClustalW MUSCLE PAGAN
Warning: PRANK is significantly more time consuming. MAFFT is the fastest.

Select the MSA algorithm     MAFFT (default) PRANK ClustalW
Warning: PRANK is significantly more time consuming. MAFFT is the fastest.

Please enter your email address (Optional)     
Your email address will be used to update you the moment the results are ready.

Job title (Optional)
Enter a descriptive job title for your GUIDANCE query

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Advanced Options

Number of bootstrap repeats    

Output order:
  Same as input
  Aligned

Genetic Code:    Nuclear Standard Nuclear Blepharisma Nuclear Ciliate Nuclear Euplotid Mitochondria Vertebrate Mitochondria Invertebrate Mitochondria Yeast Mitochondria Ascidian Mitochondria Echinoderm Mitochondria Flatworm Mitochondria Protozoan

Advanced MAFFT Options:
Max-Iterate 0 1 2 5 10 20 50 80 100 1000(long run)
Pairwise alignment method 6mer localpair genafpair globalpair

Advanced PRANK Options:
Trust insertions (+F)

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                             Show Example Results