General interface
From pfaat
What does the alignment viewer look like?
There is a screen shot of the alignment viewer below. Features are highlighted in red text.
What does the tree viewer look like?
There is a screen shot of the tree viewer below.
How do I edit the alignment?
1. To insert a gap, left click on a residue and drag the residue to the right while holding the SHIFT button. Alternatively, use the space bar.
2. To delete a gap, left click on the residue to the right of the gap and drag the residue to the left while holding the SHIFT button. Alternatively, use the backspace bar.
3. To shift multiple sequences, first select multiple sequences as described here.
What formats are supported?
Alignments:
1. pfaat - This is the format that is saved by default. We recommend using this format if you want to save a color scheme, annotations, or residue numbering. You can always save back to another format.
2. aln – CLUSTAL format
3. tfa, fa, fsa, afa – Fasta format
4. msf - GCGs msf format
5. nex - Nexus non-interleaved alignment format. Nexus alignments are saved from alignment viewer. Trees are saved separately from the tree viewer.
6. tab - A tab delimited file.
Trees:
1. nhx - This is the format that is saved by default. We recommend using this format if you want to save, annotations, bootstrap and Log L values. The New Hampshire extended format can be loaded from the alignment viewer (CTRL-T) or the tree viewer.
2. nh, ph – The New Hampshire format can be loaded from the alignment viewer (CTRL-T) or the tree viewer.
3. nex, con – The nexus tree format can be loaded from the Alignment viewer (CTRL-T) or from the tree viewer if it is already launched. The first tree is read from the .nex or .con (consensus) file. Bayesian probabilities are loaded as LogL values. The translate field is recognized but most other fields are not recognized. The tree viewer does not save nexus format trees.
How do I find a motif (pattern) in my favorite sequence?
1. Select your sequence of interest as described here. e.g. NGF_HUMAN
2. On the Find menu, click Sequence Motif… or type CTRL-M for motif.
3. Type a pattern 'e.g. 'RGE'' into the text field.
4. Click on '''Selected sequences'''.
5. Click on the '''Find''' button
6. Click the '''Cancel''' button when you are finished.
How do I select one or more residues?
1. Left click on a residue.
2. To select a range, hold the SHIFT key and click on a second residue in the same sequence.
3. To select Multiple residues in on or more sequences, hold the CTRL key and click on multiple residues.
How do I select one or more columns?
1. Select your residues of interest as described here.
2. On the '''Edit''' menu, click on '''Extend -> Residue Selection to Column''''.
3. Alternatively, hold down the CTRL or SHIFT key while left clicking on the white space immediately below the Alignment column numbers.
How do I select one or more sequences?
1. Click on the name to select one sequence.
2. CTRL-Click on the names to select multiple sequences.
3. SHIFT-Click on the names to select a range of sequences.
How do I move my favorite sequences to the top of the alignment?
1. Select your favorite sequence names as described here.
2. On the '''View''' menu, click '''Sort Sequences By: -> Selection'''.
How do I zoom in and out of the tree viewer?
Use the scroll wheel or a middle mouse button to zoom in and out. There are also zoom buttons on the bottom right of the tree viewer.
