Alignment Window Calculate Menu
+Calculate-- - +-
- Sort -
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- The Sort menu will - have some additional options if you have just done a multiple - alignment calculation, or opened a tree viewer window.- by ID
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- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-- by Group
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- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-- by Pairwise Identity
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- This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put - at the top.
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-- Calculate Tree -
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Functions for calculating trees on the alignment or the - currently selected region. See calculating trees. --
-- Average Distance Using % Identity
-- Neighbour Joining Using % Identity
-- Average Distance Using Blosum62
-- Neighbour Joining Using Blosum62
-- Pairwise Alignments
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- Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
-- Principal Component Analysis
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- Shows a spatial clustering of the sequences based on the - BLOSUM62 scores in the alignment. See Principal Component Analysis. -
-- Web Service
- - Selecting one of the following menu items starts a remote service - on compute facilities at the University of Dundee. You need a - continuous network connection in order to use these services - through Jalview. - --
-- Clustal Alignment
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- Submits all, or just the currently selected sequences for alignment with clustal W.- Clustal Realign
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- Submits the alignment or currently selected region for - re-alignment with clustal W. Use this if you have added some - new sequences to an existing alignment.- Muscle Alignment
- Submits all, or jut the currently selected sequences for - alignment using Muscle. Do not use this if you are working with - nucleic acid sequences.
-- JNet
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- Secondary structure prediction by network consensus. The - behaviour of this calculation depends on the current selection: --
-- If nothing is selected, and the displayed sequences appear to - be aligned, then a JNet prediction will be run for the first - sequence in the alignment, using the current - alignment. Otherwise the first sequence will be submitted for prediction. -
-- If - just one sequence (or a region on one sequence) has been selected, - it will be submitted to the automatic JNet prediction server - for homolog detection and prediction. -
-- If a set of sequences are selected, and they appear to be aligned, - then the alignment will be used for a Jnet prediction on the - first sequence selected in the set (that is, the one - that was first clicked on). -
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