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# 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,

Are there a list of 6 character for all standard or ‘named’ models of nucleotide substitution (e.g:010010 defines HKY85)?
Does 012345 define General Reversible Model?

Hi hs,

F81 : 000000
HKY85 : 010010
TrN93 : 010020
REV : 012345

Cheers,
Sergei

In SLAC and FEL, selecting '(3):[Estimate] Estimate from data with branch corrections(slower)' rather than '(5):[Estimate dN/dS only]' at 'dN/dS bias parameter options' tend to produce dN/dS = 0/0 rather than dN/dS = inf (∞)?
The sites with dN/dS = inf (∞) can be declared to be under positive selection if p-value < 0.05?

Hi hs,

hs wrote on Dec 7^th, 2010 at 11:44am:



1). You mean that when you provide input values to SLAC/FEL from a config list, you see the message printed on the screen? That is normal behavior: the program prints a prompt regardless of whether or not the input is provided from the console or from the pre-populated list.

2). Not directly from NucModelCompare.bf -- the file is preprogrammed to save either nothing or everything.

Sergei

Hi hs,

hs wrote on Dec 2^nd, 2010 at 10:17am:


It would appear that the likelihood function output generated by NucModelCompare.bf is not directly importable by QuickSelectionDetection.bf. The text in the book is in error. Thanks for pointing this out. If you replace NucModelCompare.bf with the file that I have attached, this should be fixed.

Thanks for the bug report!

Sergei