Question: How to get a JTT-fsite model and JTT-fgene model from JTT model provided by PAML
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gravatar for PandaGoo
2.0 years ago by
PandaGoo0
China
PandaGoo0 wrote:

I identified some convergent amino acid substitutions but didn't know how to get new models (JTT-fsite and JTT-fgene) for statistical test with CONVERG2 software. I am confused of the formula 'M=M0*πj/π0j' mentioned by a paper about 'convergent evolution'. What is the difference between JTT-Fsite and JTT-Fgene model?

  1. M0: JTT matrix M0 was provided in PAML. 20*20
  2. πj: "The equilibrium amino acid frequency vector π for a site was estimated from the observed amino acid frequencies among all taxa at the site for JTT-fsite and across all sites of the protein for JTT-fgene, respectively." I am confused about this sentence.
  3. π0j: "Given the original equilibrium frequency vector π0 determined by the JTT matrix,"

Following are example sequences provided by CONVERG2 software.

Any suggestion or calculation process would be appreciate.

Langur 
KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
Baboon
KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV
Human 
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV
Rat
KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV
Cow  
KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL
Horse
KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL

'

jtt-f model gene • 547 views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 2.0 years ago by PandaGoo0
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