Colouring by Conservation

Selecting this option causes the colour scheme to be applied to only those residues that occur in that column more than a certain percentage of the time. For instance selecting the threshold to be 100 will only colour those columns diff --git a/help/html/colourSchemes/blosum.html b/help/html/colourSchemes/blosum.html index 6749d4e..338ca55 100755 --- a/help/html/colourSchemes/blosum.html +++ b/help/html/colourSchemes/blosum.html @@ -31,7 +31,7 @@ td { -

Gaps are coloured white. If a residue matches the consensus sequence residue at that position it is coloured dark blue. If it does not match the consensus residue but the 2 residues have a positive Blosum62 score, it is coloured light diff --git a/help/html/colourSchemes/buried.html b/help/html/colourSchemes/buried.html index 1373404..5943d36 100755 --- a/help/html/colourSchemes/buried.html +++ b/help/html/colourSchemes/buried.html @@ -30,7 +30,7 @@ td { -

diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index b95a348..33455dc 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -30,7 +30,7 @@ td { -

Clustal X Colour Scheme

Clustal X Colour Scheme

This is an emulation of the default colourscheme used for alignments in Clustal X, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html index 8866435..5ceba85 100755 --- a/help/html/colourSchemes/conservation.html +++ b/help/html/colourSchemes/conservation.html @@ -21,7 +21,7 @@ --> Colouring by Conservation -

Colouring by Conservation

Colouring by Conservation

This is an approach to alignment colouring which highlights regions of an alignment where physicochemical properties are conserved. It is based on the one used in diff --git a/help/html/colourSchemes/helix.html b/help/html/colourSchemes/helix.html index e4142c1..8c698c0 100755 --- a/help/html/colourSchemes/helix.html +++ b/help/html/colourSchemes/helix.html @@ -30,7 +30,7 @@ td { -

Helix Propensity

Helix Propensity

diff --git a/help/html/colourSchemes/hydrophobic.html b/help/html/colourSchemes/hydrophobic.html index 288a2d1..6b4cf2d 100755 --- a/help/html/colourSchemes/hydrophobic.html +++ b/help/html/colourSchemes/hydrophobic.html @@ -30,7 +30,7 @@ td { -

Hydrophobicity

Hydrophobicity

According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this table are coloured red and the most hydrophilic ones are coloured blue.

diff --git a/help/html/colourSchemes/nucleotide.html b/help/html/colourSchemes/nucleotide.html index 601230b..065c818 100755 --- a/help/html/colourSchemes/nucleotide.html +++ b/help/html/colourSchemes/nucleotide.html @@ -30,7 +30,7 @@ td { -

Nucleotide Colours

Nucleotide Colours

diff --git a/help/html/colourSchemes/pid.html b/help/html/colourSchemes/pid.html index f90fde9..47b992a 100755 --- a/help/html/colourSchemes/pid.html +++ b/help/html/colourSchemes/pid.html @@ -30,7 +30,7 @@ td { -

PID Colours
+

PID Colours

The PID option colours the residues (boxes and/or text) according to the percentage of the residues in each column that agree with the consensus sequence. Only diff --git a/help/html/colourSchemes/purinepyrimidine.html b/help/html/colourSchemes/purinepyrimidine.html index 6655392..4337d48 100644 --- a/help/html/colourSchemes/purinepyrimidine.html +++ b/help/html/colourSchemes/purinepyrimidine.html @@ -30,7 +30,7 @@ td { -

Purine/Pyrimidine Colours

Purine/Pyrimidine Colours

diff --git a/help/html/colourSchemes/strand.html b/help/html/colourSchemes/strand.html index a653c8e..fe7c469 100755 --- a/help/html/colourSchemes/strand.html +++ b/help/html/colourSchemes/strand.html @@ -30,7 +30,7 @@ td { -

Strand propensity

Strand propensity

diff --git a/help/html/colourSchemes/taylor.html b/help/html/colourSchemes/taylor.html index 268915d..a5c4f05 100755 --- a/help/html/colourSchemes/taylor.html +++ b/help/html/colourSchemes/taylor.html @@ -30,7 +30,7 @@ td { -

Taylor

Taylor

These colours were invented by Willie Taylor and an entertaining description of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)

diff --git a/help/html/colourSchemes/turn.html b/help/html/colourSchemes/turn.html index ec65d6f..87dbe37 100755 --- a/help/html/colourSchemes/turn.html +++ b/help/html/colourSchemes/turn.html @@ -30,7 +30,7 @@ td { -

Turn propensity

Turn propensity

diff --git a/help/html/colourSchemes/zappo.html b/help/html/colourSchemes/zappo.html index 01d2b37..db025c0 100755 --- a/help/html/colourSchemes/zappo.html +++ b/help/html/colourSchemes/zappo.html @@ -30,7 +30,7 @@ td { -

Zappo Colours
+

Zappo Colours

The residues are coloured according to their physicochemical properties as follows:

-- 1.7.10.2