【博士论文】Treefam数据库的建立.pdf

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1、TreeFamêâ¥ïáoð£nØÔn;¤µx*¥IÆnØÔn¤ÁµTreeFamÓÄÏê⥴'uÄÏ[x?zêâ¥"§åuuФ²L<ó§O(q¢]§Jø¤k®ÄÔÄÏ[x?z{§±9XÓXÓ&E"3muTreeFamêâ¥L§¥§·Oo#L{±Jpï?zäO(599Ïêâ¥ï"1{´å{"½A½fäÿÀ§ù{±p?zäØUC½fäÿÀ(¶ù<ó(J±±3"1´!:ü{"3xä§ù{y!:±C½^S3²¡ü§l¦qäx3¡þkXqÀúJ"1n{´íäÄÏO/"{"3ùÜ©¥§·rc<íä{B\nص

2、e§¿òÙí2uÔ«äõ©/"ÄÏO/"íä{VÇ/ª3ùÙ?Ø"1o{´äÜ¿{§§(ÜõlÓS8EÄÏä§ÏL~íäÑO/"¯ÚÀJpgÐ

3、±ï`äl¤kÀä"3©Ù(Äuý¢êâµÿL²äÜ¿{±wÍJpïäO(5¶ù¯¢`²µ¦+{{4q,{óO(§§EØOål{"«{pÖ¿´O(ïä'"TreeFamê⥴http://www.treefam.org§3¥Iºhttp://treefam.genomics.org.cn"'cµ©f?z§?zä§êâ¥ConstructingtheTreeFamdatabaseLiHeng

4、(MajorinTheoreticalPhysics)DirectedbyZhengWei-mouTheInstituteofTheoreticalPhysicsChineseAcademicofScienceAbstract:TreeFamisadatabaseofphylogenetictreesofgenefamilies.Itaimstodevelopacuratedresourcethatpresentstheaccurateevolutionaryhistoryofallanimalgenefamilies,aswellasreliableorthologsandparalo

5、gassignment.IndevelopingTreeFam,fournovelalgorithmsweredesignedtoimprovetheaccuracyoftreebuildingortoservespecialneedsfordevelopment.Thefirstisaconstrainedneighbour-joiningthatefficientlyaddsnewsequencestoanexistingtreewhilemaintainingtheoriginaltopologyatthesametime.Thismethodisusedtoexpandaseedtre

6、etoafulltreewithoutlosinganyinformationaddedbymanualcuration.Thesecondalgorithmisaleafreorderingthatorderstheleavesofatreeaccordingtotheweightsofleaves.Whenitisdrawnasapicture,onetreecanbedisplayedindifferentways,dependingontheorderofleaves.Thisalgorithmhelpstodisplaytreesinaconsistentalgorithmand

7、facilitatesvisualexaminationoftrees,whichisparticularlyhelpfulwhencomparingtwotrees.Thirdly,duplicationandlossinferenceisfitintoamoregeneraltheoreticalframeworkandextendedtoallowforamultifurcatedspeciestree.Afourthalgorithmhasalsobeendeveloped,whichisanewalgorithmformergingtrees.Thetreemergealgori

8、thmitselfisnotatreebuildingalgorithm,butitreconstructsanoptimaltreefromseveraltreesthatarebuiltfromanidenticalsequencesetwithdifferenttreebuildingmethods.Theresultanttreeshouldcombinetheadvantagesof,andsooutperform,allt