false alarm on duplications

[Li Pingchuan]

the RAxMLHPC-MPI-AVX warning me five duplication found, but actually there is no duplication in it. 

for example,

IMPORTANT WARNING: Sequences Traes_2AL_993ED6D63.1  and Traes_2AL_993ED6D631.1  are Exactly identical

lipch @ MBMORDR646278: ~ / tmp $ grep "Traes_2AL_993ED6D63.1" input.phy

Traes_2AL_993ED6D63.1 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAKGEREGRLP-LLLLLLVLCLLAQSRIAAAATHPQDAAALKS---LMRKWSNVPASWRK-KSNDPCGDR------------------WDGIECNGAN-----SRVTSLNLFGMNMKG-------------------------------TLSDDIGSLTELRVLDLSSNKDLGGP-LTPAIG-------------------------KLVQLINLALIGCSFSGTVPSELGNLA----QLEFFGLNSNQFTGRIPP--SLGKLSKVKWLDLADNKLTG---------------------LLPNSRDNGAGLDQLLNAEHFHLNQNSLEGPIP---EYMFNSSMNLKHILLDRNNLSG-TIPSS--IGLIPT-LEVLRLNNNNFT-------------------------------------------------GRVPAMNNLTKLHVLML-SNNKLSGPMP-NLTDMNG--------------------------LGNVDLSNNSF--TPSGVP---SWFTELPGLMTLTMQSV---GISGKLPQKLFGLRDLQ--HVILNDNELNDTLDMGNNINDGLDL-VDLRNNKITSVTVYSSLDSKLLK-----LEGNPLCTDSLLSNTLLC----TDQLAEFPIMLPFSDVQCPHPFVETIFFRSPSFGDVRKFLP------ELHDNLSRTVSSC----------------------TPNKLGLV---------------------PYVDDV--YLKVDIKACPVNQKRFNYSQVLNCFN-LTLQTYKPPENFGPYYV-------------KSHPY-PFHDKAS-----RAILIGVVTGSVLLVVGLALIGLYAVRQKKRAKMLVSQNNP------------------------------FASWGSTPEDIGEAP-KLKSAR---------AFTLEELKLSTNDFK-QINAIGEGGYGTVYRGKLL---DGQ----------LIAIKRSKQ---GSMQG--------------------------GLEFKTEIELLSRV-----HHNNLVGLVGFCFE-----KGEK--MLVYEFISNGTLSEALYGM------------------KGVQLDWSMRLQIALDSARGLAYLHDHA------------------NPPIIHRDIKSTN--ILLDS--KMT-AKVA----DFGLSLL--VSDSE-----------EGELCTNVKGT----------------------LGYLDP----EYYM---TQQ-------LTAKSDVYSFGVVLLELIVANPPIYEKK----------------YIVREVKTALDMEDTMY--CG--------LKDVMDPVLYKMGG-----LLGFPRFVTMALQCVEEVG-PDRPKMNNVVREIEMIMQDNGLTPGSMSASSSFSVDSTTRTFAPRYPYSSTSTPSTTYQMDSRAFEYSGGFPSQGSLKNRNTSPKPRSSRERGLPG

do I have to ignore them?

thanks,

[Alexandros Stamatakis]

can you send me the command line you used and the input file please?

alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org