Phylogeny:INT LTR retroelements

From The Gypsy Database

GalEa1Cico1Olco1Zeco1Zeco2pCalTdh2Ty4Tkm1Tse1Ty2Ty1BCoDi5.6CoDi5.1CoDi5.2CoDi5.3CoDi5.4CoDi5.5CoDi7.1CoDi2.4CoDi3.1CoDi4.4CoDi4.1CoDi4.3CoDi4.5Endovir1-1SIRE1-4ToRTL1TSI-9Opie-2Vitico1-2MelmothHopscotchRetrofitKoalaTork4Tnt-1V12Tto1BatataRTvr2Sto-4FourfTricopia1731XanthiaspCretro3pCretro6HumnumMtangaYokozunaCopiaKocoPocoOryco1-1Vitico1-1AracoOryco1-2CoDi6.6CoDi6.1CoDi6.7CoDi6.4CoDi6.5CoDi6.2CoDi6.3Hydra1-1Hydra1-2PyRE1G1OsserSaci-6SinbadKobelNinjaBelRooMaxTribelNabelMooseSpirobelHydra3-1Cer10-1TasCer7MabelPurbelSuzuGabelZebelTamyCubelSURLGulliverCer4Cer6Cer5MagSPMCFG1Hydra2-1DRMCigr-1SnRVRTVL-IaHERV-EREVBAEVMMuLVRCHO-K1FeLVPERV-MSLMdEVGALVKoRVWdSVXEN1ASSBSVZFERV-2ZFERVJSRVMMTVK-HERVHERV-K10SMRV-HSERVMPMVSRV-1PyERVLPDVRSVBLVHTLV-1HTLV-2STcLV2PP1664CAEVVMVSA-OMVVEIAVBIVFIVSIVMNDSIVAGMHIV-1SIVMACHIV-2DrFV-1MuERV-LFFVBFVEFVSFV-1HFVTor4aTedZamTv1Idefix17.6Tom297NomadBurdockSpringerGypsyGypsyvirHMS-BeagleYoyoMicropiaBlastopiaMdg3Tor2Tor1rGmr1Gmr1OsvaldoWootCirceUlyssesCinful-1RetroSor1B1147A04.5RIRE2Grande1-4OgreTft2Tat4-1Bagy-2Athila4-1DiasporaCalypsoCyclops-2KabukiCsRN1BoudiccaCer1Cer3Cer2Mdg1412G-RhodoTse3PeabodyDelTmaLegolasRetrosat-2Bagy-1GaladrielMonkeyTntom1GloinReinaGimliIfg7Beetle1CerebaCRMTy3-1SkipperTF2TF1Cft-1SkippyCgretPyretAmn-ichiAmn-sanSushi-ichiAmn-niMaggyDane-1marY1MGLR3GrasshopperRealPyggyINT ltr retroelements.png

Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the integrases and transposases included in the GIN/GINGER category. Phylogenetic analysis performed with the PHYLIP 3.6 package, 100 bootstrap replicates and JTT substitution model for aminoacid replacement. Here is shown the consensus tree obtained from MRC method.

 

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