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HYPHY Package >> HyPhy feedback >> Interpreting rel. dS units between HYPHY and PAML http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1126272230 Message started by avilella on Sep 9th, 2005 at 6:23am |
Title: Interpreting rel. dS units between HYPHY and PAML Post by avilella on Sep 9th, 2005 at 6:23am
Interpreting rel. dS units between HYPHY and PAML
Dears, I have a dataset for which I have tested the Local/FR and Global/M0 models of codons in HYPHY and PAML for the Codon Frequency models that they share in their implementation, and found that: Both programs give exactly (to the fourth/fifth decimal) the same results, in the Likelihood Value, R/omegas, dN/dS values, tree branch lengths, etc. Both programs use, as expected, different units in the branch lengths of the estimated tree, in a relation of 3 to 1 or to number of changes per codon or per nucleotide. Both programs use different units in the dS (and dN for Local/FR) branch lengths that don't follow a 3 to 1 relationship, and this relation changes between the different shared Codon Frequency models or between subsets of the data. I would like to know how to interpret this difference in units in absolute terms between the programs. Here an example: ~2.09 to 1 relation Global/M0 = HYPHY / PAML / Tkodak.synRate=5.61358 / 2.6837 2.0917316 Pfurio.synRate=2.22195 / 1.0622 2.0918377 Node4.synRate=1.13503 / 0.5426 2.0918356 Pabyss.synRate=1.88494 / 0.9010 2.0920533 Phorik.synRate=1.64998 / 0.7887 2.0920249 Local/FR = HYPHY / PAML / TKODAK.nonSynRate=0.338324 / 0.1619 2.0897097 ; =0.0480279146887137 TKODAK.synRate =7.04432 / 3.3721 2.0890009 PFURIO.nonSynRate=0.141819 / 0.0679 2.0886451 ; =0.0569279865125241 PFURIO.synRate =2.4912 / 1.1924 2.0892318 Node4.nonSynRate=0.0775024 / 0.0371 2.0890135 ; =0.898580634389877 Node4.synRate =0.0862498 / 0.0413 2.0883729 PABYSS.nonSynRate=0.110662 / 0.0530 2.0879623 ; =0.0519508199030106 PABYSS.synRate =2.13013 / 1.0196 2.0891820 PHORIK.nonSynRate=0.10045 / 0.0481 2.0883576 ; =0.0600953628754839 PHORIK.synRate =1.67151 / 0.8001 2.0891264 ######################################## Due to the constraints of the forum thread, I've emailed more details on the analysis to Sergei emails account. Thanks in advance, Albert. |
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