X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=34e8d758a08db746e546a56c595bb498135edeab;hb=309af01a4a460b17ef6b924a20057b372d8fbeac;hp=a1c630e5e12d837794cf4e316076e31d1798e2c1;hpb=de255c8c87707a2cd2a2a15f5ad04ed10fe5846d;p=jalview.git diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index a1c630e..34e8d75 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -24,35 +24,35 @@ -

- Alignment Window Calculate Menu -

Sort -
- 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 Length
  This will sort - the sequences according to their length (excluding gap - characters). 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. -
- The Sort - menu will have some additional options if the alignment has any - associated score annotation, or you have just done a multiple - alignment calculation or opened a tree viewer window.

+ Alignment Window Calculate Menu +

Sort +
- 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 Length
  This will + sort the sequences according to their length (excluding gap + characters). 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.
- The Sort + menu will have some additional options if the alignment + has any associated score annotation, or you have just done a + multiple alignment calculation or opened a tree viewer + window. +
Calculate Tree
Functions for calculating trees on the alignment or the currently selected region. See calculating @@ -74,35 +74,58 @@
Average Distance Using % Identity

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 similarity scores calculated over the alignment.. See Principal - Component Analysis.
-
Extract Scores ... (optional)
This - option is only visible if Jalview detects one or more white-space - separated values in the description line of the alignment sequences.
- When selected, these numbers are parsed into sequence associated - annotation which can then be used to sort the alignment via the Sort - by→Score menu.
-
Translate as cDNA (not applet)
This option is visible for nucleotide alignments. - Selecting this option shows the DNA's calculated protein product in a new split frame window. Note that the - translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the - standard genetic code (any incomplete final codon is discarded). - You can perform this action on the whole alignment, - or selected rows, columns, or regions.
-
Get Cross-References (not applet)
This option is visible where sequences have cross-references to - other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries. - Select the database to view all cross-referenced sequences in a new split frame window.
-
Autocalculate Consensus
For - large alignments it can be useful to deselect "Autocalculate - Consensus" when editing. This prevents the sometimes lengthy - calculations performed after each sequence edit.
-
Sort Alignment With New Tree
If - this option is selected, the alignment will be automatically sorted - whenever a new tree is calculated or loaded.
-
+ Smith and Waterman algorithm to selected sequences. See pairwise alignments. +

Principal Component Analysis
Shows + a spatial clustering of the sequences based on similarity scores + calculated over the alignment.. See Principal Component Analysis. +
Extract Scores ... (optional)
This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +
Translate as cDNA (not applet)
+ This option is visible for nucleotide alignments. Selecting + this option shows the DNA's calculated protein product in a new + split frame window. + Note that the translation is not frame- or intron-aware; it + simply translates all codons in each sequence, using the + standard genetic code + (any incomplete final codon is discarded). You can perform this + action on the whole alignment, or selected rows, columns, or + regions. +
Reverse, Reverse Complement (not applet)
+ These options are visible for nucleotide alignments. Selecting them adds the reverse (or reverse complement) + of the sequences (or selected region) as new sequences in the alignment. To try this out, add this sequence and + perform 'Reverse Complement' followed by 'Translate as cDNA': +
+ Seq GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC + TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG +
Get Cross-References (not applet)
+ This option is visible where sequences have + cross-references to other standard databases; for example, an + EMBL entry may have cross-references to one or more UNIPROT + entries. Select the database to view all cross-referenced + sequences in a new split + frame window. +
Autocalculate Consensus
For + large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This prevents + the sometimes lengthy calculations performed after each sequence + edit.
Sort Alignment With New Tree
If + this option is selected, the alignment will be automatically + sorted whenever a new tree is calculated or loaded.
Show Flanking Regions
Opens a new alignment window showing any additional sequence data either side of the current alignment. Useful in conjunction with