HyPhy message board - How to assess more than two compartments?

rbjmax

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How to assess more than two compartments?
Feb 24^th, 2011 at 12:59pm

I just attended the workshop in Vancouver, thank you so much Sergei! I am very excited to apply what I learned to my system, which was lacking some of the sophisticated analysis available through HyPhy. why, here's one now!

I have a large dataset of viral sequences. each sequence comes from a field isolate for which I have a lot of specific data. I would like to assess the extent of compartmentalization in this data, and I have at least 4 different parameters that might yield interesting compartmentalization patterns. For each parameter, though, I have at least three categories (i.e. host age parameter can be either adult, juvenile, or unknown)while others have as many as 6-8 categories. When I try the standard compartmentalization analysis with my newly formatted data, I find that I am only prompted to enter two clade names, which seems to be forcing me to using only two compartments. naturally our tutorial didn't suffer this problem since all our exercise were for two compartments only!
p.s. my data is unaligned equal length sequences in fasta format.
thanks!

Rachel

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Sergei

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Re: How to assess more than two compartments?
Reply #1 - Feb 24^th, 2011 at 3:08pm

Hi Rachel,

The only analysis that supports >2 compartments out of the box is Slatkin-Maddison. To use it, align your sequences, build a tree on them and then feed the tree (in a Newick format) into the SM analysis. For F_ST, I would suggest you do pairwise comparisons at this stage, although the analysis can be modified to accept > 2 compartments in principle.

Sergei

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rbjmax YaBB Newbies Offline Feed your monkey! Posts: 17	Re: How to assess more than two compartments? Reply #2 - Feb 24^th, 2011 at 3:11pm Thanks, Sergei!
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rbjmax YaBB Newbies Offline Feed your monkey! Posts: 17	Re: How to assess more than two compartments? Reply #3 - Jun 15^th, 2011 at 1:43pm finally getting back on to this question- I have a tree, but the newick formatted tree is annotated with a ton of extra information- will this be a problem in HyPhy?
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Sergei

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Re: How to assess more than two compartments?
Reply #4 - Jun 15^th, 2011 at 1:48pm

Can you paste a portion of the tree in for me to look at? There COULD be an issue with some annotations.

rbjmax wrote on Jun 15^th, 2011 at 1:43pm:

finally getting back on to this question- I have a tree, but the newick formatted tree is annotated with a ton of extra information- will this be a problem in HyPhy?

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rbjmax

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Re: How to assess more than two compartments?
Reply #5 - Jun 15^th, 2011 at 2:03pm

hope this isn't too big a chunk:
(((((((((((((((((((((2008_mG169M:2.1036091078962293,2008_mG170M:2.10360910789622
93):1.0059222134082226,2008_mG168M:3.109531321304452):2.201174981731981,2006_mG1
73M:3.310706303036433):0.34253394108839785,2008_mG167M:5.653240244124831):1.2776
411478423313,(2008_mG192M:3.4069212229937804,2008_mG205M:3.4069212229937804):3.5
239601689733817):1.991352249421162,(((2009_mG172M:2.4493631466027956,2010_mG190M
:3.4493631466027956):3.967227998412813,(2007_mG191M:3.367975029503935,2006_mG146
M:2.367975029503935):1.048616115511674):0.17169055461077676,2008_mG175M:5.588281
6996263855):3.3339519417619385):0.36101251841867565,(((((2009_mG188M:3.150117993
6136765,2010_mG206M:4.1501179936136765):1.52355070776024,2009_mG186M:4.673668701
373916):2.179117506277798,2003_mG139M:0.8527862076517145):2.2296030713126207,200
4_mG157M:4.082389278964335):0.2957054660698333,2002_mG110M:2.3780947450341685):0
.9051514147728312):0.2896151967647178,((((2009_mG171M:3.507108424753099,2009_mG1
82M:3.507108424753099):1.4547251861966402,(2009_mG183M:2.159077769720888,2009_mG
178M:2.159077769720888):2.8027558412288514):1.945740623886568,(2006_mG158M:2.123
53323745878,2010_mG189M:6.12353323745878):1.7840409973775273):2.7420674134981233
,2003_mG156M:3.6496416483344305):0.923219708237287):2.006133126764535,

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to assess more than two compartments? Reply #6 - Jun 15^th, 2011 at 2:05pm Those look like standard branch lengths, should not be a problem.
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rbjmax

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Re: How to assess more than two compartments?
Reply #7 - Jun 15^th, 2011 at 2:09pm

this is the other kind I usually have, far more annotation:

((((1971_mG208L[&rate_range={1.872986442721916E-4,0.001869756643050936},height_95%_HPD={39.0,39.000000000000014},length_range={0.0190377240984958,15.461154188740153},height_median=39.00000000000001,length_95%_HPD={0.05424389529628115,6.278075690308768},height=39.0,rate=7.736151296744967E-4,height_range={38.999999999999986,39.00000000000003},rate_median=7.626642320805635E-4,length=2.626851194657905,length_median=2.1584160725403123,rate_95%_HPD={4.632194965990371E-4,0.0010824400452709737}]:2.143027088494229,1971_mG209L[&rate_range={2.6132835912544527E-4,0.002267323146212564},height_95%_HPD={39.0,39.000000000000014},length_range={0.024959823260523706,17.643963584779755},height_median=39.00000000000001,length_95%_HPD={0.05424389529628115,6.302494019079504},height=39.0,rate=7.935345313839731E-4,height_range={38.999999999999986,39.00000000000003},rate_median=7.77482153987292E-4,length=2.6371934052934014,length_median=2.162182485154375,rate_95%_HPD={5.046010337144174E-4,0.0011251166573838405}]:2.143027088494229)[&height_95%_HPD={39.05424389529629,45.12781181304712},length_range={0.013868511334969469,25.874891981782078},length_95%_HPD={0.44387166965020697,11.496605183667853},height_range={39.024959823260524,52.60776950134397},rate_95%_HPD={4.5709659211972217E-4,0.0010710414759673753},rate_range={2.3221001928602186E-4,0.0030272973865627614},height_median=41.143027088494236,rate=7.811044246609478E-4,height=41.58444063265806,posterior=0.987376577927759,rate_median=7.681600340178988E-4,length=5.719257996129565,length_median=5.378014293152042]:4.436094804458023,1969_mG207L

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Sergei

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Re: How to assess more than two compartments?
Reply #8 - Jun 15^th, 2011 at 2:11pm

If you put that in a NEXUS file, then HyPhy can parse the comments (in []) correctly, i.e. do

Code:

#NEXUS
BEGIN TREES;
TREE T = ((((1971_mG208L[&rate_range={1.872986442721916E-4,0.001869756643050936},height_95%_HPD={39.0,39.000000000000014},length_range={0.0190377240984958,15.461154188740153},height_median=39.00000000000001,length_95%_HPD={0.05424389529628115,6.278075690308768},height=39.0,rate=7.736151296744967E-4,height_range={38.999999999999986,39.00000000000003},rate_median=7.626642320805635E-4,length=2.626851194657905,length_median=2.1584160725403123,rate_95%_HPD={4.632194965990371E-4,0.0010824400452709737}]:2.143027088494229,1971_mG209L[&rate_range={2.6132835912544527E-4,0.002267323146212564},height_95%_HPD={39.0,39.000000000000014},length_range={0.024959823260523706,17.643963584779755},height_median=39.00000000000001,length_95%_HPD={0.05424389529628115,6.302494019079504},height=39.0,rate=7.935345313839731E-4,height_range={38.999999999999986,39.00000000000003},rate_median=7.77482153987292E-4,length=2.6371934052934014,length_median=2.162182485154375,rate_95%_HPD={5.046010337144174E-4,0.0011251166573838405}]:2.143027088494229)[&height_95%_HPD={39.05424389529629, ...
END;

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rbjmax YaBB Newbies Offline Feed your monkey! Posts: 17	Re: How to assess more than two compartments? Reply #9 - Jun 15^th, 2011 at 2:13pm sweet, thanks Sergei!
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