X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fcalculations.html;fp=help%2Fhtml%2Fcalculations%2Fcalculations.html;h=c194cd93c9ac0314e9dcb0c74d1a815d09be9970;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git diff --git a/help/html/calculations/calculations.html b/help/html/calculations/calculations.html new file mode 100644 index 0000000..c194cd9 --- /dev/null +++ b/help/html/calculations/calculations.html @@ -0,0 +1,55 @@ + + + +The Alignment Calculations Dialog + + +

+ The Alignment Calculations Dialog +

+ Alignment Calculations dialog box - opened via Calculations->Tree or PCA... +

+ The Calculations Dialog (shown above) is opened via + the Calculations→Calculate Tree or PCA... + menu entry. +

+

+ It allows you to select the type of alignment analysis calculation (PCA or Tree), and the + sequence similarity score model that will be used to perform the + analysis. +

+

+ Adding additional score models
Jalview can + import substitution matrices in both AAindex + and NCBI format (see e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/). + In Jalview 2.10.2, the easiest way to import new models is to drag + the score model file onto any alignment window. See the Substitution Matrices Documentation + for more information. +

+ +