From: Jim Procter Date: Fri, 2 Oct 2020 16:27:09 +0000 (+0100) Subject: fix up ‘enabling group consensus’ in column-based subgroup conservation analysis... X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=125aedebd6511841069df08f212087236b0f705d fix up ‘enabling group consensus’ in column-based subgroup conservation analysis exercise and mention ‘recommended column’ for creating subgroups --- diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index e437288..c8111d1 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -2987,9 +2987,8 @@ the pattern of unlinked nodes in the tree display.} tree based conservation analysis exercise (exercise \ref{consanalyexerc}).} \exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to create a new view. Ensure the annotation panel is displayed ({\sl Annotations $\Rightarrow$ Show Annotations} is toggled on). Enable the -display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$ -Autocalculated Annotation $\Rightarrow$ -Group Consensus} submenu.} +display of consensus annotation rows for each group by selecting the {\sl Group Consensus} option in the {\sl Annotation $\Rightarrow$ +Autocalculated Annotation } submenu.} \exstep{Displaying the sequence logos will make it easier to see the different residue populations within each @@ -2999,7 +2998,8 @@ mouse and dragging it up. Alter its position, by right clicking the name of the and dragging it up to the top of the annotations.} \exstep{In the column alignment ruler, select a column exhibiting with about 50\% of its residues conserved ({\em ie. about 50\% in the consensus histogram}) - that lies within the central conserved region of the alignment.} + that lies within the central conserved region of the alignment. + (Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).} \exstep{Subdivide the alignment according to this selection using {\sl Select $\Rightarrow$ Make Groups for Selection}.} \exstep{Re-order the alignment according to the new groups that have been