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MultAlign: Multiple Sequence Alignment Tools

Note: We are currently working on a new implementation of this page. We suggest you use the AllAll page instead. 

Filling and submitting this form (see also the example) will do one or several of the following: score your alignment, recalculate the alignment using different methods, construct trees, calculate the probabilistic anestral sequence (PAS) or create an alignment based on domains 

The result should be mailed to:
(Email address)
Title of your job (optional):

Seperate your sequences and labels either with ';' or ':'. The labels are optional.
The sequences may contain '_' or '-' as gaps. You can enter the sequences as follows:

  • SwissProt ID's, e.g. CRFR_HUMAN, CRFR_MOUSE etc 
  • Accession number, e.g. P22796, P22797, etc 
  • Sequences with or without gaps, e.g. VLFLRL______RSIRCLRNIIHWN, LFLRLRPGCTHWGDQADG, etc 
Labels Multiple Sequence Alignment


Desired results (default is the calculation of the score):
Score: Just score the given alignment, no recalculation is done
GapAdjust: Adjust the gaps with our new gap adjustment function
ProbModel: (Re)calculate the alignment with the probabilistic model (gap adjustment)
Repeated:(Re)calculate the alignment with the Repeated Pairwise Model (gap adjustment)
RootedTree: Rooted phylogenetic tree using ProbModel 
UnrootedTree: Unrooted phylogenetic tree using ProbModel
TSPTree: rooted tree using a TSP method 
FitchTree: rooted tree using FITCH of the PHYLIP package 
ProbAncestral: Probabilistic ancestral sequence (Please do not use this selection. It is not working properly and you will not receive any of your results if you do)

ClustalWGap: Recalculate the alignment using ClustalW (WITH gap adjustment)
MSAGap: Recalculate the alignment using MSA 2.1 (WITH gap adjustment)

Other sites:
Questions, problems, suggestions? Check out the 
CBRG 
 
Comments, questions, problems? darwin.comments@inf.ethz.ch
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