Alignment Window Calculate Menu
- Sort
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
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
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
This will sort the selected sequences by their percentage identity to the consensus sequence. The most similar sequence is put at the top.
- Calculate Tree
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
Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
- Principal Component Analysis
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
Submits all, or just the currently selected sequences for alignment with clustal W.- Clustal Realign
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
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).