Phylogeny:AP LTR retroelements


Tork4Sto-4BatataV12Tnt-1RTvr2Tto1FourfCopiaKocoYokozunaMtangaHumnumpCretro3PyRE1G1TricopiaHydra1-2Hydra1-1pCretro6Xanthias1731MelmothVitico1-1PocoOryco1-1Oryco1-2AracoToRTL1Opie-2TSI-9Endovir1-1SIRE1-4Vitico1-2KoalaHopscotchRetrofitOsserCoDi5.1CoDi5.2CoDi5.3CoDi5.6CoDi5.4CoDi5.5CoDi6.5CoDi6.7CoDi6.6CoDi6.1CoDi6.2CoDi6.3CoDi6.4Tse1pCalTdh2Ty4Tkm1Ty2Ty1BCoDi2.4CoDi3.1CoDi4.5CoDi4.3CoDi4.4CoDi7.1CoDi4.1Zeco2Zeco1Olco1Cico1GalEa1CalypsoCyclops-2Athila4-1DiasporaBagy-2Grande1-4RIRE2B1147A04.5RetroSor1Cinful-1OgreTat4-1Tft2Cer5Cer6Cer4SURLMagDRMSPMCFG1Hydra2-1GulliverCigr-1Cer2Cer3Cer1LegolasTmaDelPeabodyBagy-1Retrosat-2Tntom1MonkeyGaladrielGimliIfg7GloinReinaCerebaCRMBeetle1G-RhodoREM1CgretPyretSkippyCft-1MaggyDane-1marY1Sushi-ichiAmn-sanAmn-niAmn-ichiMGLR3PyggyRealTy3-1SkipperTF2TF1Tse3OsvaldoWootCirceUlyssesGmr1rGmr1XEN1ZFERV-2SnRVASSBSVZFERVWdSVRCHO-K1MuLVFeLVBAEVMPERV-MSLREVMdEVKoRVGALVHERV-ERTVL-IaHTLV-1HTLV-2BLVMPMVSRV-1SERVSMRV-HJSRVK-HERVHERV-K10MMTVRSVLPDVPyERVMuERV-LSIVMACHIV-2HIV-1SIVMNDSIVAGMEIAVFIVCAEVSA-OMVVVMVBIVMdg3BlastopiaMdg1412MicropiaYoyoHMS-BeagleNomadGypsyvirGypsyBurdockSpringerTom29717.6IdefixTv1ZamTedSFV-1HFVBFVEFVFFVDrFV-1NabelTribelBelRooMaxMooseCer7MabelTasSpirobelHydra3-1Cer10-1Saci-6SinbadKobelNinjaTamyPaoZebelCubelGabelSuzuPurbelTor2Tor1Tor4aBoudiccaKabukiCsRN1BRRVCSVMVSbCMVPCSVTVCVLLDAVCaMVCERVMiMVFMVSVBVEVCVRuFDVCmYLCVSbCMVBRRVPCSVRTBVPVCVCSVMVBSGFVBSVAVBSOLVKTSVBSMyVCLNVComYMVDrMVScBIMVBSCVBVTaBVDBVCYMVCSSVGrasshopperSTcLV2PP1664AP retroel 2a.png
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Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the protease protein (AP) -encoded by the pol internal region common to Ty3/Gypsy, Retroviridae, Bel/Pao, Caulimoviridae and Ty1/Copia LTR retroelement families- and on a second non-pol protease-like domain, encoded by the ORF7 of three soymoviruses and by the C-terminus of CSVMV-ORF I Cavemovirus (downstream to the MOV region) (highlighted in red). The tree has been reconstructed using Felsenstein´s protein sequence parsimony method based on (Eck and Dayhoff 1966) and (Fitch 1971) to generate a majority-rule consensus tree (Margush and McMorris 1981). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference

 




Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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