Phylogeny:POL LTR retroelements

From The Gypsy Database

Vitico1-2MelmothOpie-2SIRE1-4ToRTL1AracoRTvr2Tto1V12KoalaRetrofitHopscotchEndovir1-1BatataTnt-1Tork4Sto-4FourfOsserCoDi6.2CoDi6.3CoDi6.5CoDi6.4CoDi6.6CoDi6.7CoDi6.1CoDi7.1CoDi2.4CoDi4.5CoDi3.1CoDi4.1CoDi4.3CoDi4.4Tdh2pCalSinbadKobelYokozunaZebelTy2Ty1BMaxGabelSpirobelCer7SuzuHydra3-1MoosePurbelCubelTasMabelTribelBelCer10-1RooSaci-6NabelLPDVJSRVSMRV-HSERVRSVHTLV-2STcLV2PP1664SRV-1MPMVK-HERVHTLV-1MMTVBLVTat4-1PyERVHERV-K10RCHO-K1SA-OMVVZFERV-2IdefixTomHIV-1EIAVCer6Cinful-1MuLVFFVMdEVGALVZamPERV-MSLFeLVGrande1-4KoRVB1147A04.5RetroSor1Bagy-2MicropiaTv1Gypsy297Athila4-1YoyoTedMuERV-LMdg117.6Cyclops-2Tft2ScBIMV412BlastopiaMdg3CYMVKTSVCLNVBSVAVOgreRIRE2CalypsoBSMyVDrMVBSOLVHMS-BeagleBurdockBSGFVCSSVmarY1GrasshopperTaBVTVCVSushi-ichiDBVRTBVNomadAmn-niPyggyBsCVBVCer1RealAmn-sanTy3-1ComYMVAmn-ichiPyretDane-1CerebaSkippyTF2TF1SkipperMGLR3Ifg7Bagy-1GloinMonkeyCft-1MaggyReinaTntom1CgretTse3Beetle1GimliREM1CSVMVDiasporaLLDAVRuFDVTor4aGaladrielCer2TmaPeabodyCRMEVCVG-RhodoPVCVMiMVCERVCmYLCVRetrosat-2FMVCaMVDelPCSVSVBVHydra2-1MagSPMBRRVLegolasGypsyvirSpringerCer5Cer4GulliverSURLSbCMVCer3SnRVDRMOsvaldoBAEVMCFG1HERV-ERTVL-IaBoudiccaCsRN1UlyssesGmr1Tor2WootrGmr1REVCigr-1KabukiTor1CirceFIVSFV-1EFVWdSVBFVHFVDrFV-1ZFERVSIVAGMSIVMNDASSBSVXEN1Ty4VMVSIVMACCAEVHIV-2BIVTamyCoDi5.3CoDi5.1CoDi5.2PaoNinjaCoDi5.6CoDi5.5Zeco1Zeco2TSI-9CoDi5.4Olco1Cico1CopiaKocoMtangaHydra1-2Hydra1-1pCretro6pCretro31731TricopiaOryco1-1Vitico1-1PocoOryco1-2GalEa1Tse1Tkm1PyRE1G1XanthiasHumnumPol ltr retroelement.png

Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the concatenated protein product encoded by the pol internal region common to Ty3/Gypsy, Retroviridae, Bel/Pao, Caulimoviridae and Ty1/Copia LTR retroelements families using MEGA 4.1 (Kumar et al. 2008) and the Neighbor joining (NJ) method of phylogenetic reconstruction (Saitou and Nei 1987) with 100 bootstrap replicates under the conditions uniform rates among sites and pairwise deletion of gaps.

 

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