From 7028eac3a32db980f3e04014fd18a2ab3b1a52ff Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 21 Jun 2019 17:27:30 +0100 Subject: [PATCH 1/1] =?utf8?q?JAL-3111=20added=20Colour=20By=20ID=20and=20an?= =?utf8?q?=20overview=20of=20Jalview=E2=80=99s=20alignment=20colouring=20cap?= =?utf8?q?abilities?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/help/html/colourSchemes/index.html | 717 ++++++++++++++++--------------- 1 file changed, 373 insertions(+), 344 deletions(-) diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html index 51d0738..f0ae161 100755 --- a/help/help/html/colourSchemes/index.html +++ b/help/help/html/colourSchemes/index.html @@ -49,355 +49,384 @@ td { a new scheme in the Colour menu.

The "Colour→Colour Text..." + href="textcolour.html">Colour Text..." entry opens a dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.

-

The default colour schemes are summarised in the table below: -

-

 

-

- Protein Colour Schemes -

- - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ARNDCQEGHILKMFPSTWYVBXZ
Clustal
Zappo
Taylor
Hydrophobicity
Helix Propensity
Strand Propensity
Turn Propensity
Buried Index
-
-

 

-

- Nucleotide Colour Schemes -

- - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ACGTUIXRYNWSMKBHDV
Nucleotide
Purine/Pyrimidine
-
+

+ Dynamic colour schemes +

+

+ Alignments and groups may be coloured according to associated sequence and alignment + annotation. Any applied colour schemes (such as those shown in the + table below) can also be shaded by + amino acid physico-chemical property conservation to reveal patterns + of variation, or applied selectively to Above + Identity Threshold. +

+

+ Alignments and groups can also be shaded according to percentage + abundance of aligned residues (using Percentage + Identity), and for protein alignments, the BLOSUM + 62 Score and ClustalX shading schemes + highlight amino acid conservation. +

+

+ The Sequence ID colour scheme shades sequences with + the same colour assigned to their Sequence ID. Colours are assigned + when groups are created by partitioning + a tree or subdividing the alignment by sequence with Select→Make + Groups For Selection. +

+

+ Amino acid and Nucleotide based colour schemes +

The built-in colour schemes based on amino acid and nucleotide symbols are + summarised in the table below: + +

 

+

+ Protein Colour Schemes +

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ARNDCQEGHILKMFPSTWYVBXZ
Clustal
Zappo
Taylor
Hydrophobicity
Helix Propensity
Strand Propensity
Turn Propensity
Buried Index
+
+

 

+

+ Nucleotide Colour Schemes +

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ACGTUIXRYNWSMKBHDV
Nucleotide
Purine/Pyrimidine
+
-
-

 

+
+

 

-- 1.7.10.2