NGPhylogeny.fr

Clustal Omega 1.2.4_1

Sequences file

Sequence type

Dealign input sequences

If given already aligned sequences, by default Clustal Omega use the existing alignment to guide creation of the new alignment, by constructing a HMM from the existing alignment. Check this box to realign aligned sequences from scratch.

Clustering guide-tree

By default, only a fraction of the distance matrix is calculated, for speed. Calculate full matrix may be more accurate under some circumstances but is slower and needs more memory.

Use iteration

Redo the alignment multiple times to improve accuracy. Both the HMM and the guide tree will be recalculated each time.

Calculate full distance matrix during iteration

Number of iterations (combined guide-tree/HMM)

Different number of guide tree, HMM iterations

Normally, if iteration is specified, a new guide tree and HMM will be calculated for each iteration. Use this option to restrict the number of iterations for either.

Maximum guide tree iterations

Maximum number of HMM iterations

MSA output order

Display tree guide

Alignment Output format

References to cite

2011

Fabian Sievers and Andreas Wilm and David Dineen and Toby J Gibson and Kevin Karplus and Weizhong Li and Rodrigo Lopez and Hamish McWilliam and Michael Remmert and Johannes Söding and Julie D Thompson and Desmond G Higgins. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7:539