Here are some questions for Exercise in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
.
# 2.3.4 Previewing trees in HyPhy
It is stated that 'HyPhy can plot the tree in several conventional styles (e.g. slanted, radial) that are selected from the ‘Tree Style’ tab, but defaults to plotting ‘rectangular’ trees as shown in Fig. 2.2.', but only 'Rectangular' is shown at 'Tree Style' with my tree files on Mac OS X (10.5.8).
# 2.3.5 Making an alignment
when I Execute StandardAnalyses>Data File Tools>SeqAlignment.bf, after choosing 'No' in the window called 'Insert a coordinate reference sequence?', the three windows ('Sequence File', 'Include outliers', and 'Try reverse complements?') appear before 'Choose Genetic Code'. updated?
# 2.3.6 Estimating a tree
'Use MeanPairwiseDivergence' for which tree? 'Inferred_Tree' or 'InfluenzaA_H3_fixed_fas_nuc_Inferred_Tree'?
it is stated that 'Save the results via File>Save choosing Include sequence data, NEXUS option from the pull down menu in the file dialog'. I did it on the window called 'DataSet InfluenzaA_H3_fixed_fas' out of the four windows. correct?
# 2.4.1 Fitting a global model in the HyPhy GUI
it is stated that 'Finally, save the likelihood function with all parameter estimates by switching back to the data panel, executing File>Save>Save, and choosing Include sequence data, NEXUS as a format option in the save dialog.' I did it on the window called 'DataSet InfluenzaA_H3_Random352' out of the five windows. correct?
# 2.5.1 Fitting a local codon model in HyPhy
'select the topology included with file' indicates which of 'MammalsBirds_tree' or 'MammalsBirds_TREE'?
I invoked 'Likelihood>Enter Command' and typed:
global globalRatio=1;ReplicateConstraint("this1.?.nonSynRate:=globalRatio*this2.?.synRa
te",MammalsBirds_tree,MammalsBirds_tree);
I selected (Likelihood>Optimize LF) because I cannot invoke (Likelihood>Optimize).
# 2.6.3 Single-likelihood ancestor counting (SLAC)
I invoke 'Standard Analyses > Positive Selection > QuickSelectionDetection.bf',
for the 'Ancestor Counting Options' dialog, I selected 'Single Ancestor Counting' because I cannot find 'Single likelihood ancestor'.
'the codon has an expected 1.1 synonymous sites (out of 3)' - why 3?
'this scaling enables the comparison across different datasets' - Scaled dN-dS calculated from different genes and different number of taxa can be compared?
# 2.6.4 Fixed effects likelihood (FEL)
How to (i) conduct a FEL analysis with the same settings except test for selection only within the mammalian clade, rooted at internal node Node4, and (ii) do a 'branch-site' type analysis on Node4?
# $typo =~ s/Yabg/Yang/;
(5) Test for positive selection using the approach of Nielsen and Yabg,
would read
(5) Test for positive selection using the approach of Nielsen and Yang,