GUIDANCE Server - a web server for assessing alignment confidence score

Compute multiple sequence alignment confidence score

Select algorithm

More details about each algorithm in the overview section.

GUIDANCE is not suitable for alignments of very few sequences.
As a rule of thumb, use GUIDANCE3 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)

Select sequences type

Amino Acids

Nucleotides

Codons

Select input type

Select the MSA algorithm

Warning: PRANK is significantly more time-consuming than MAFFT.

Note: Alternative MAFFT algorithms (e.g. L-INS-i: localpair + maxiterate 1000) can be configured via Advanced Options below — however, some are considerably slower.

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.

Advanced Options

Number of alternative guide-trees

Disable convergence — always generate 4 alternative alignments per guide-tree (N × 4 total, where N is the number of guide-trees specified above), instead of stopping early when scores stabilise

Output order

Same as input

Aligned

Genetic Code:

Advanced MAFFT Options:

Max-Iterate

Pairwise alignment method

Alternative MAFFT algorithms can be configured as follows:
L-INS-i: localpair + maxiterate 1000
G-INS-i: globalpair + maxiterate 1000
E-INS-i: genafpair + maxiterate 1000
FFT-NS-i (≥2 cycles): 6mer + maxiterate i (e.g. 2 or 1000)
Note: iterative methods are considerably slower than the default FFT-NS-2.

Advanced PRANK Options:
Trust insertions (+F)