Dear Yer,
There are several tests described in the PLoS paper (Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
).
1). Test for selection along internal branches at every site of a given sample. This can be achieved by Standard Analyses->Positive Selection->QuickSelectionDetection->...->Two Rate FEL -> ... -> Internal Branches Only (when prompted for branch class).
2). Differential IFEL - compare strengths of selection along internal branches at each site of two samples. Standard Analyses->PositiveSelection->CompareSelectivePressureIVL.bf
3). Given a sample, and a partitioning of codons into two non-overlapping (but not necessarily covering the entire sequence) sets, test whether the mean strength of selection along internal branches differs between the two sets (Population Level Adaptation Test). This is not included in standard analyses, but you can do it like this.
Run an IFEL analysis from (1). This will generate a nucleotide fit file among other things. When you look at the results of IFEL, partition all codons into those which (i) Have only tip dN > 0 (ii) Have internal branch dN>0. You need to generate a file that looks like
Code:partSpec={};partSpec["Tips"]="18-20,36-38,48-50,51-53,63-65,69-71,84-86,126-128,180-182,183-185,186-188,189-191,213-215,2
16-218,225-227,240-242,243-245,291-293,294-296,297-299,303-305,312-314,318-320,372-374,375-377,384-386,390-392,396-398,40
5-407,408-410,411-413,414-416,423-425,435-437,438-440,450-452,453-455,459-461,462-464,468-470,471-473,489-491,504-506,549
-551,561-563,573-575,576-578,579-581,582-584,585-587,588-590,591-593,594-596,597-599";
partSpec["Internals"]="6-8,21-23,24-26,57-59,123-125,171-173,246-248,282-284,351-353,363-365,399-401,465-467,477-479,483-
485,498-500,510-512";
I'll write a little script which takes the output of IFEL and generates it for you and post it later today (hopefully).
With the nucleotide fit and the partition file, now download Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
and feed it the two files for the IFEL LRT test.
Hopefully this helps,
Sergei
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