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ݧ֧ܧڧ 14 phylo

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Valery Korneyev
Valery Korneyev

Computative Phylogenetics. Nexus format. PAUP*

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ڧߧڧ ٧ݧ?ߧ? ڧ֧ާѧڧܧ ߧާ֧ߧܧݧѧ ֧ܧ? 1 4
3 . NDE C NEXUS Data Editor (by Roderic D.M.PAGE, 2001) ֧էѧܧ ާѧڧ ާѧ ? NEXUS (ӧڧܧڧӧ? PAUP, WinClada, PAST) . ѧէ٧ӧڧѧ ߧ էاߧ ? ݧ֧ԧܧ ܧڧӧѧߧ?, է٧ӧݧ? ?էܧݧѧ ? ڧߧܧ, ԧ? ѧܧ ѧۧݧ էݧ ?ߧ֧ѧܧڧӧߧڧ ӧڧ٧ߧѧߧڧ? ާѧ? DELTA.
3 . NDE C NEXUS Data Editor (by Roderic D.M.PAGE, 2001) ֧էѧܧ ާѧڧ ާѧ ? NEXUS (ӧڧܧڧӧ? PAUP, WinClada, PAST) . ѧէ٧ӧڧѧ ߧ էاߧ ? ݧ֧ԧܧ ܧڧӧѧߧ?, է٧ӧݧ? ?էܧݧѧ ? ڧߧܧ, ԧ? ѧܧ ѧۧݧ էݧ ?ߧ֧ѧܧڧӧߧڧ ӧڧ٧ߧѧߧڧ? ާѧ? DELTA.
ާѧ NEXUS (*.nex) ѧէ٧ӧڧѧۧߧ ٧ӧڧߧڧ ? ܧݧѧէߧڧ ާѧ ѧۧ? ާѧڧާ, ڧܧѧާ ѧܧ?, ٧ߧѧ ?? ѧ?, ѧܧ ܧާѧߧ, ҧ ٧ҧݧ֧ߧڧ էݧ ӧڧܧڧѧߧߧ ԧѧ? PAUP . ?ڧ ߧѧҧѧԧѧ ?ݧ ҧݧ?, ? *.mtr ѧҧ *.ss . #NEXUS BEGIN TAXA; DIMENSIONS NTAX=53; TAXLABELS balli foveum argenteolum lapponicum punctatostriatum hesperium lorquinii zephyrum l._levettei l._carrianum inaequale litorale conicolle Asa._alaskanum ; ENDBLOCK;
ާѧ NEXUS (*.nex) BEGIN CHARACTERS; DIMENSIONS NCHAR= 10 ; FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="012345678"; CHARLABELS [1] silver_spots [2] interval_3_micro. [3] 'interval_4+5_micro.' [4] 'interval_6+7_micro.' [5] outer_mirror [6] silver_spot [7] elytral_microsculpture [8] suborbital_setae [9] midlat._pron._seta [10] 'ed3_+_ed5_+_3rd' ; STATELABELS 1 absent present, 2 absent v._slight_mirrors slight_mirrors distinct_mirrors, 3 absent v._slight_mirrors slight_mirrors distinct_mirrors, 4 absent v._slight_mirrors slight_mirrors distinct_mirrors, 5 joined isolated, 6 restricted_to_3rd also_on_4th, 7 isodiametric slightly_trans. transverse, 8 absent 'short_+_sparse_denser' _, 9 absent present, 10 on_3rd_interneur in_interval, ; MATRIX balli 1110-00(12)10 foveum 1110-00(12)10 argenteolum 13(23)(01)-00200 alaskense 13(23)0-(01)0200 semenovi 1220-00200 stenoderum 133(02)000(12)00 carinula 13(012)0-00210 velox 13(012)1-00210 lapponicum 13(0123)(02)000210 punctatostriat 13(012)1-00010 ; ENDBLOCK;
ާѧ NEXUS (*.nex) BEGIN NOTES; [Taxon comments] [Character comments] [Character state comments] [Attribute comments] [Taxon pictures] PICTURE TAXON=2 FORMAT=GIF SOURCE=FILE PICTURE='imagesoveum.gif'; [Character pictures] [Character state pictures] [Attribute pictures] ENDBLOCK;
ާѧ NEXUS (*.nex) BEGIN PAUP; Outgroup balli; set maxtrees = 100; set criterion = likelihood; bootstrap nreps=100; hs; contree; savetree; ENDBLOCK;
3 . PAUP (Phy l ogenetic Analaysis Using Parsimony) ( ѧӧ - David L. Swofford) ԧѧ ߧѧڧѧߧ էݧ MacOS; PAUP * 4.0b10 for 32-bit MS Windows (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) է٧ӧݧ? ѧߧѧ?٧ӧѧ էѧ? ٧ էާԧ ߧ ?ݧܧ ާ֧է ѧڧާ?? , ѧݧ ѧܧ ާ֧? ߧѧۧ?ݧ? ѧӧէ?ҧߧ? ( maximum likelihood ) ֧??ӧܧԧ ѧߧѧ?٧ ( Bayesian analysis ). ҧڧէӧ ? ާ֧է ӧڧܧڧӧ է֧ѧݧߧ ѧӧѧ? ֧ӧݧ?ۧ? ާէ֧?. ֧ ާѧܧڧާѧݧߧ? ѧӧէ?ҧߧ? ?ڧ?٧? ?ާ?? ڧާѧߧߧ էѧߧڧ, ֧?ԧѧ ֧ѧݧߧ?, ѧ ֧??ӧܧڧ ѧߧѧ? ?է? ?ߧܧ ۧާ?ߧ? ܧاߧԧ է֧֧ӧ, էѧ ֧٧ݧѧ? ܧѧڧߧ ڧ֧ߧߧ (٧?ݧ) ۧާ?ߧ֧. ާ ? ֧֧ .. "??է֧֧-ާէ֧ݧ֧" ҧڧ ߧѧӧާѧߧߧ. ? ? ?ߧڧ ާ֧ ٧ѧҧڧ? ߧ֧ӧڧ٧ߧѧ֧ߧ ?ݧ? ѧ, ާ ڧѧߧߧ, ܧݧ ѧާ ٧ڧߧڧ ҧѧߧ, ? ?ݧܧ է?ݧߧڧ. ڧ ߧ ާ֧ߧ, ҧڧէӧ ާ֧է?ܧѧ٧ ֧٧ݧѧ?, ܧ??էڧާܧ ާ? ܧاߧ ?ݧܧ.? ? ?֧٧, ٧ҧݧ֧? ߧ ߧ? ڧ ާ֧?, ? ?ݧܧ ٧ڧާ ? ѧܧڧާ, ?էէѧ ֧֧??. ӧݧ?ۧߧ ާէ֧ݧ, ٧ ߧ֧ҧ?էߧ?, ާاߧ ܧݧѧէߧӧѧ. ѧѧާ֧ ާէ֧? ?ߧ ҧ֧٧֧֧էߧ ӧڧէ էѧߧߧڧ, ߧ? ٧ѧܧݧѧէѧ, ާ ާاߧ ߧڧܧѧ ڧ֧ߧ ӧڧէ? ֧ӧݧ??
ا ֧ݧ٧֧ߧ֧ۧ ( Joe Felsenstein ) ֧?? ѧ֧ ?էէѧ ܧڧڧ? ާ֧ ѧڧާ?? ܧݧѧէڧڧ?, ӧ֧էا, ֧ӧݧ? ߧ ٧ѧӧاէ ۧէ ާڧ ݧ ? ?ҧ? ާ֧է, ? է٧ӧݧ ?ߧڧ ѧӧէ?ҧ? ֧ӧݧ?ۧߧڧ ާէ֧ݧ֧, ߧѧ? ܧ ӧߧ ߧ ? ߧѧۧ?ݧ ?ާ?ߧڧާ. ? ٧ѧߧӧѧ ާ֧ ާѧܧڧާѧݧߧ? ѧӧէ?ҧߧ? (Maximum likelihood) . ֧??ӧܧڧ ѧߧѧ? ( Bayesian analysis) է٧ӧݧ? ٧ էާԧ ֧ӧߧ? ֧֧ާ ?ߧڧ ?ާ?? ԧ ?ߧԧ է֧֧ӧ է ?ӧѧӧݧ֧ߧߧ էѧߧߧڧާ (ѧ?ߧ) ? ѧ C ?ݧ ?ӧѧӧݧ֧ߧߧ էѧߧڧާ (ѧ֧?ߧ) . PAUP* է٧ӧݧ? ӧէڧ ѧܧ ֧??ӧܧڧ ѧߧѧ? . ѧڧާ? , ҧ ާ֧ ߧѧ֧ۧܧߧާ?? ?֧٧ (٧ ٧ѧާӧӧѧߧߧ), ާѧܧڧާѧݧߧ ѧӧէ?ҧ? ֧??ӧܧڧ ѧߧѧ? C ߧӧ? ѧݧ֧ߧѧڧӧ? ܧڧ֧??, ? ӧڧܧڧѧ? PAUP* էݧ ?ߧܧ ֧ӧݧ?ۧߧڧ ?֧ .
3 . PAUP * 4.0b10 for 32-bit MS Windows ֧? ܧާѧߧէ: (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) ݧ֧ާ֧ߧѧ? ܧާѧߧէ : BandB ; (Branch and Bound Search) C ѧާ, bb HENNIG86 hs ; (Heuristic Search) ѧާ, ie HENNIG86 contree ; (Consensus Tree) C ڧҧݧڧ٧ߧ ѧާ, nelsen , ѧݧ է٧ӧݧ ߧ էڧ, 4 ?٧? ڧ ܧߧ֧ߧߧڧ է֧֧: ֧ݧ?ӧ? (?), էѧާ?, ߧѧ?ӧ? ܧߧ֧ߧ ?ݧ? SaveTrees File=C: .. Filename.tre ; Outgroup [taxon]; - ӧڧ? ٧ӧ?ߧ? ԧ. ?է?ߧ ? TreeGardener, ڧݧ֧ߧ? ܧާѧߧէ ?ҧߧ ٧ѧէѧӧѧ ܧާѧߧէߧާ էܧ (ѧҧ ߧѧ֧֧ ڧӧѧ ? ҧݧ? PAUP Nexus ѧۧݧ.
3 . PAUP * 4.0b10 for 32-bit MS Windows ֧? ܧާѧߧէ: (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) ݧ֧ާ֧ߧѧ? ߧѧҧ ܧާѧߧ ҧݧ? PAUP: Outgroup [taxon]; hs; contree; SaveTrees File=C:ilename.tre Format=Nexus; Outgroup [taxon]; hs; contree; SaveTrees File=C:ilename.tre Format=Nexus; ѧҧ: Outgroup [taxon]; BootStrap Search=BandB; SaveTrees File=C:ilename.tre Format=Nexus; ѧҧ: Outgroup [taxon]; set maxtrees = 100; set criterion = likelihood; bootstrap nreps=100 ; SaveTrees File=C:ilename.tre Format=Nexus; (էݧ ӧ֧ݧڧܧڧ ާѧڧ ߧܧݧ֧ڧէߧڧ ٧ߧѧ) ?է?ߧ ? TreeGardener, ڧݧ֧ߧ? ܧާѧߧէ ?ҧߧ ٧ѧէѧӧѧ ܧާѧߧէߧާ էܧ (ѧҧ ߧѧ֧֧ ڧӧѧ ? ҧݧ? PAUP Nexus ѧۧݧ.
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3 . PAUP * 4.0b10 for 32-bit MS Windows ֧? ܧާѧߧէ: (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) ?? էݧ HSearch: contree strict = YES |NO ٧ѧާӧӧѧߧߧ, strict = YES . ڧܧڧӧۧ STRICT = NO ?է?ߧڧ ?. S emistrict = YES|NO ڧҧ֧? S emistrict = YES , ڧާѧ ߧѧ?ӧԧ ܧߧ֧ߧߧ է֧֧ӧ (ܧާ?ߧӧѧߧ? ܧާߧ֧ߧ) M aj R ule = YES|NO ڧҧ֧? M aj R ule = YES ڧާѧ ܧߧ֧ߧߧ է֧֧ӧ ٧ ѧӧڧݧ ?ݧ? (٧ ٧ѧާӧӧѧߧߧ, 50%) Adams = YES|NO ڧҧ֧? Adams = YES ڧާѧ ܧߧ֧ߧߧ է֧֧ӧ ٧ ѧӧڧݧ ?ݧ? (٧ ٧ѧާӧӧѧߧߧ, 50%)
4. BioEdit ( ѧӧ C Tomas A. Hall ) ԧѧ է٧ӧݧ? ԧѧ?٧ӧӧѧ ߧڧ٧ܧ ?ܧӧ֧ߧ? ѧܧڧ ڧߧ, ? ާاߧ էѧ? ֧֧ӧӧѧ NEXUS ާѧ էݧ էѧݧԧ ܧݧѧէڧڧߧԧ ѧߧѧ?٧. 1. ڧާѧ NCBI ҧ?ܧӧѧ? ?ܧӧ֧ߧ (ѧҧ ӧݧѧ?) ? ӧڧܧݧѧ ? ߧӧڧ ѧۧ.
4. BioEdit ( ѧӧ C Tomas A. Hall ) ԧѧ է٧ӧݧ? ԧѧ?٧ӧӧѧ ߧڧ٧ܧ ?ܧӧ֧ߧ? ѧܧڧ ڧߧ, ? ާاߧ էѧ? ֧֧ӧӧѧ NEXUS ާѧ էݧ էѧݧԧ ܧݧѧէڧڧߧԧ ѧߧѧ?٧. 2. ާ֧ߧ: Accessory Application C ClustalW Multiple alignment .
4. BioEdit ( ѧӧ C Tomas A. Hall ) 3 . ѧܧ? էէѧ CLUSTAL, ܧڧ ѧӧާѧڧߧ ӧڧڧܧӧ? ߧܧݧ֧ڧէ ߧѧۧ?ݧ ?ާ?ߧڧ ?.
4. BioEdit ( ѧӧ C Tomas A. Hall ) 4 . ܧݧ֧ڧէ ӧڧڧܧӧ, ާ ߧ ?? ۧާ?ߧڧ է֧ݧ֧? ӧ ?ݧ .
4. BioEdit ( ѧӧ C Tomas A. Hall ) 5 . ֧? ?էӧߧ? ٧? ֧էѧԧӧѧ ӧߧ ? ܧѧܧӧާ ? ӧڧԧݧ?.
4. BioEdit ( ѧӧ C Tomas A. Hall ) 6 . ҧ?٧?ާ ?ӧ? ҧ ҧ?.
4. BioEdit ( ѧӧ C Tomas A. Hall ) 7 . ܧ?ާ NEXUS ާѧ ( *.nex) .
4. BioEdit ( ѧӧ C Tomas A. Hall ) 8 . ѧۧ ާ? ѧܧڧ ӧڧԧݧ ? ԧӧڧ է ѧߧѧ?٧ ٧ էާԧ PAUP
4. BioEdit ( ѧӧ C Tomas A. Hall ) 8 . ѧۧ ާ? ѧܧڧ ӧڧԧݧ ? ԧӧڧ է ѧߧѧ?٧ ٧ էާԧ PAUP
5 . PAST ( ѧӧ C Tomas A. Hall )
ѧۧӧѧاݧڧ? ?֧ѧ: 1. Parsimony, Phylogeny and Genomics . 2005. Albert,V.A. (ed.) C Oxford Univ. Press, New York. ix + 229 p. 2. Lipscomb, D. 1998. Basics of Cladistic Analisys . G.Washington Univ., Washington, D.C. 75 p.

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ݧ֧ܧڧ 14 phylo

  • 1. ڧߧڧ ٧ݧ?ߧ? ڧ֧ާѧڧܧ ߧާ֧ߧܧݧѧ ֧ܧ? 1 4
  • 2. 3 . NDE C NEXUS Data Editor (by Roderic D.M.PAGE, 2001) ֧էѧܧ ާѧڧ ާѧ ? NEXUS (ӧڧܧڧӧ? PAUP, WinClada, PAST) . ѧէ٧ӧڧѧ ߧ էاߧ ? ݧ֧ԧܧ ܧڧӧѧߧ?, է٧ӧݧ? ?էܧݧѧ ? ڧߧܧ, ԧ? ѧܧ ѧۧݧ էݧ ?ߧ֧ѧܧڧӧߧڧ ӧڧ٧ߧѧߧڧ? ާѧ? DELTA.
  • 3. 3 . NDE C NEXUS Data Editor (by Roderic D.M.PAGE, 2001) ֧էѧܧ ާѧڧ ާѧ ? NEXUS (ӧڧܧڧӧ? PAUP, WinClada, PAST) . ѧէ٧ӧڧѧ ߧ էاߧ ? ݧ֧ԧܧ ܧڧӧѧߧ?, է٧ӧݧ? ?էܧݧѧ ? ڧߧܧ, ԧ? ѧܧ ѧۧݧ էݧ ?ߧ֧ѧܧڧӧߧڧ ӧڧ٧ߧѧߧڧ? ާѧ? DELTA.
  • 4. ާѧ NEXUS (*.nex) ѧէ٧ӧڧѧۧߧ ٧ӧڧߧڧ ? ܧݧѧէߧڧ ާѧ ѧۧ? ާѧڧާ, ڧܧѧާ ѧܧ?, ٧ߧѧ ?? ѧ?, ѧܧ ܧާѧߧ, ҧ ٧ҧݧ֧ߧڧ էݧ ӧڧܧڧѧߧߧ ԧѧ? PAUP . ?ڧ ߧѧҧѧԧѧ ?ݧ ҧݧ?, ? *.mtr ѧҧ *.ss . #NEXUS BEGIN TAXA; DIMENSIONS NTAX=53; TAXLABELS balli foveum argenteolum lapponicum punctatostriatum hesperium lorquinii zephyrum l._levettei l._carrianum inaequale litorale conicolle Asa._alaskanum ; ENDBLOCK;
  • 5. ާѧ NEXUS (*.nex) BEGIN CHARACTERS; DIMENSIONS NCHAR= 10 ; FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="012345678"; CHARLABELS [1] silver_spots [2] interval_3_micro. [3] 'interval_4+5_micro.' [4] 'interval_6+7_micro.' [5] outer_mirror [6] silver_spot [7] elytral_microsculpture [8] suborbital_setae [9] midlat._pron._seta [10] 'ed3_+_ed5_+_3rd' ; STATELABELS 1 absent present, 2 absent v._slight_mirrors slight_mirrors distinct_mirrors, 3 absent v._slight_mirrors slight_mirrors distinct_mirrors, 4 absent v._slight_mirrors slight_mirrors distinct_mirrors, 5 joined isolated, 6 restricted_to_3rd also_on_4th, 7 isodiametric slightly_trans. transverse, 8 absent 'short_+_sparse_denser' _, 9 absent present, 10 on_3rd_interneur in_interval, ; MATRIX balli 1110-00(12)10 foveum 1110-00(12)10 argenteolum 13(23)(01)-00200 alaskense 13(23)0-(01)0200 semenovi 1220-00200 stenoderum 133(02)000(12)00 carinula 13(012)0-00210 velox 13(012)1-00210 lapponicum 13(0123)(02)000210 punctatostriat 13(012)1-00010 ; ENDBLOCK;
  • 6. ާѧ NEXUS (*.nex) BEGIN NOTES; [Taxon comments] [Character comments] [Character state comments] [Attribute comments] [Taxon pictures] PICTURE TAXON=2 FORMAT=GIF SOURCE=FILE PICTURE='imagesoveum.gif'; [Character pictures] [Character state pictures] [Attribute pictures] ENDBLOCK;
  • 7. ާѧ NEXUS (*.nex) BEGIN PAUP; Outgroup balli; set maxtrees = 100; set criterion = likelihood; bootstrap nreps=100; hs; contree; savetree; ENDBLOCK;
  • 8. 3 . PAUP (Phy l ogenetic Analaysis Using Parsimony) ( ѧӧ - David L. Swofford) ԧѧ ߧѧڧѧߧ էݧ MacOS; PAUP * 4.0b10 for 32-bit MS Windows (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) է٧ӧݧ? ѧߧѧ?٧ӧѧ էѧ? ٧ էާԧ ߧ ?ݧܧ ާ֧է ѧڧާ?? , ѧݧ ѧܧ ާ֧? ߧѧۧ?ݧ? ѧӧէ?ҧߧ? ( maximum likelihood ) ֧??ӧܧԧ ѧߧѧ?٧ ( Bayesian analysis ). ҧڧէӧ ? ާ֧է ӧڧܧڧӧ է֧ѧݧߧ ѧӧѧ? ֧ӧݧ?ۧ? ާէ֧?. ֧ ާѧܧڧާѧݧߧ? ѧӧէ?ҧߧ? ?ڧ?٧? ?ާ?? ڧާѧߧߧ էѧߧڧ, ֧?ԧѧ ֧ѧݧߧ?, ѧ ֧??ӧܧڧ ѧߧѧ? ?է? ?ߧܧ ۧާ?ߧ? ܧاߧԧ է֧֧ӧ, էѧ ֧٧ݧѧ? ܧѧڧߧ ڧ֧ߧߧ (٧?ݧ) ۧާ?ߧ֧. ާ ? ֧֧ .. "??է֧֧-ާէ֧ݧ֧" ҧڧ ߧѧӧާѧߧߧ. ? ? ?ߧڧ ާ֧ ٧ѧҧڧ? ߧ֧ӧڧ٧ߧѧ֧ߧ ?ݧ? ѧ, ާ ڧѧߧߧ, ܧݧ ѧާ ٧ڧߧڧ ҧѧߧ, ? ?ݧܧ է?ݧߧڧ. ڧ ߧ ާ֧ߧ, ҧڧէӧ ާ֧է?ܧѧ٧ ֧٧ݧѧ?, ܧ??էڧާܧ ާ? ܧاߧ ?ݧܧ.? ? ?֧٧, ٧ҧݧ֧? ߧ ߧ? ڧ ާ֧?, ? ?ݧܧ ٧ڧާ ? ѧܧڧާ, ?էէѧ ֧֧??. ӧݧ?ۧߧ ާէ֧ݧ, ٧ ߧ֧ҧ?էߧ?, ާاߧ ܧݧѧէߧӧѧ. ѧѧާ֧ ާէ֧? ?ߧ ҧ֧٧֧֧էߧ ӧڧէ էѧߧߧڧ, ߧ? ٧ѧܧݧѧէѧ, ާ ާاߧ ߧڧܧѧ ڧ֧ߧ ӧڧէ? ֧ӧݧ??
  • 9. ا ֧ݧ٧֧ߧ֧ۧ ( Joe Felsenstein ) ֧?? ѧ֧ ?էէѧ ܧڧڧ? ާ֧ ѧڧާ?? ܧݧѧէڧڧ?, ӧ֧էا, ֧ӧݧ? ߧ ٧ѧӧاէ ۧէ ާڧ ݧ ? ?ҧ? ާ֧է, ? է٧ӧݧ ?ߧڧ ѧӧէ?ҧ? ֧ӧݧ?ۧߧڧ ާէ֧ݧ֧, ߧѧ? ܧ ӧߧ ߧ ? ߧѧۧ?ݧ ?ާ?ߧڧާ. ? ٧ѧߧӧѧ ާ֧ ާѧܧڧާѧݧߧ? ѧӧէ?ҧߧ? (Maximum likelihood) . ֧??ӧܧڧ ѧߧѧ? ( Bayesian analysis) է٧ӧݧ? ٧ էާԧ ֧ӧߧ? ֧֧ާ ?ߧڧ ?ާ?? ԧ ?ߧԧ է֧֧ӧ է ?ӧѧӧݧ֧ߧߧ էѧߧߧڧާ (ѧ?ߧ) ? ѧ C ?ݧ ?ӧѧӧݧ֧ߧߧ էѧߧڧާ (ѧ֧?ߧ) . PAUP* է٧ӧݧ? ӧէڧ ѧܧ ֧??ӧܧڧ ѧߧѧ? . ѧڧާ? , ҧ ާ֧ ߧѧ֧ۧܧߧާ?? ?֧٧ (٧ ٧ѧާӧӧѧߧߧ), ާѧܧڧާѧݧߧ ѧӧէ?ҧ? ֧??ӧܧڧ ѧߧѧ? C ߧӧ? ѧݧ֧ߧѧڧӧ? ܧڧ֧??, ? ӧڧܧڧѧ? PAUP* էݧ ?ߧܧ ֧ӧݧ?ۧߧڧ ?֧ .
  • 10. 3 . PAUP * 4.0b10 for 32-bit MS Windows ֧? ܧާѧߧէ: (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) ݧ֧ާ֧ߧѧ? ܧާѧߧէ : BandB ; (Branch and Bound Search) C ѧާ, bb HENNIG86 hs ; (Heuristic Search) ѧާ, ie HENNIG86 contree ; (Consensus Tree) C ڧҧݧڧ٧ߧ ѧާ, nelsen , ѧݧ է٧ӧݧ ߧ էڧ, 4 ?٧? ڧ ܧߧ֧ߧߧڧ է֧֧: ֧ݧ?ӧ? (?), էѧާ?, ߧѧ?ӧ? ܧߧ֧ߧ ?ݧ? SaveTrees File=C: .. Filename.tre ; Outgroup [taxon]; - ӧڧ? ٧ӧ?ߧ? ԧ. ?է?ߧ ? TreeGardener, ڧݧ֧ߧ? ܧާѧߧէ ?ҧߧ ٧ѧէѧӧѧ ܧާѧߧէߧާ էܧ (ѧҧ ߧѧ֧֧ ڧӧѧ ? ҧݧ? PAUP Nexus ѧۧݧ.
  • 11. 3 . PAUP * 4.0b10 for 32-bit MS Windows ֧? ܧާѧߧէ: (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) ݧ֧ާ֧ߧѧ? ߧѧҧ ܧާѧߧ ҧݧ? PAUP: Outgroup [taxon]; hs; contree; SaveTrees File=C:ilename.tre Format=Nexus; Outgroup [taxon]; hs; contree; SaveTrees File=C:ilename.tre Format=Nexus; ѧҧ: Outgroup [taxon]; BootStrap Search=BandB; SaveTrees File=C:ilename.tre Format=Nexus; ѧҧ: Outgroup [taxon]; set maxtrees = 100; set criterion = likelihood; bootstrap nreps=100 ; SaveTrees File=C:ilename.tre Format=Nexus; (էݧ ӧ֧ݧڧܧڧ ާѧڧ ߧܧݧ֧ڧէߧڧ ٧ߧѧ) ?է?ߧ ? TreeGardener, ڧݧ֧ߧ? ܧާѧߧէ ?ҧߧ ٧ѧէѧӧѧ ܧާѧߧէߧާ էܧ (ѧҧ ߧѧ֧֧ ڧӧѧ ? ҧݧ? PAUP Nexus ѧۧݧ.
  • 12. ?
  • 13. 3 . PAUP * 4.0b10 for 32-bit MS Windows ֧? ܧާѧߧէ: (ӧߧڧ ڧ ߧ http://paup.csit.fsu.edu/Cmd_ref_v2.pdf ) ?? էݧ HSearch: contree strict = YES |NO ٧ѧާӧӧѧߧߧ, strict = YES . ڧܧڧӧۧ STRICT = NO ?է?ߧڧ ?. S emistrict = YES|NO ڧҧ֧? S emistrict = YES , ڧާѧ ߧѧ?ӧԧ ܧߧ֧ߧߧ է֧֧ӧ (ܧާ?ߧӧѧߧ? ܧާߧ֧ߧ) M aj R ule = YES|NO ڧҧ֧? M aj R ule = YES ڧާѧ ܧߧ֧ߧߧ է֧֧ӧ ٧ ѧӧڧݧ ?ݧ? (٧ ٧ѧާӧӧѧߧߧ, 50%) Adams = YES|NO ڧҧ֧? Adams = YES ڧާѧ ܧߧ֧ߧߧ է֧֧ӧ ٧ ѧӧڧݧ ?ݧ? (٧ ٧ѧާӧӧѧߧߧ, 50%)
  • 14. 4. BioEdit ( ѧӧ C Tomas A. Hall ) ԧѧ է٧ӧݧ? ԧѧ?٧ӧӧѧ ߧڧ٧ܧ ?ܧӧ֧ߧ? ѧܧڧ ڧߧ, ? ާاߧ էѧ? ֧֧ӧӧѧ NEXUS ާѧ էݧ էѧݧԧ ܧݧѧէڧڧߧԧ ѧߧѧ?٧. 1. ڧާѧ NCBI ҧ?ܧӧѧ? ?ܧӧ֧ߧ (ѧҧ ӧݧѧ?) ? ӧڧܧݧѧ ? ߧӧڧ ѧۧ.
  • 15. 4. BioEdit ( ѧӧ C Tomas A. Hall ) ԧѧ է٧ӧݧ? ԧѧ?٧ӧӧѧ ߧڧ٧ܧ ?ܧӧ֧ߧ? ѧܧڧ ڧߧ, ? ާاߧ էѧ? ֧֧ӧӧѧ NEXUS ާѧ էݧ էѧݧԧ ܧݧѧէڧڧߧԧ ѧߧѧ?٧. 2. ާ֧ߧ: Accessory Application C ClustalW Multiple alignment .
  • 16. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 3 . ѧܧ? էէѧ CLUSTAL, ܧڧ ѧӧާѧڧߧ ӧڧڧܧӧ? ߧܧݧ֧ڧէ ߧѧۧ?ݧ ?ާ?ߧڧ ?.
  • 17. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 4 . ܧݧ֧ڧէ ӧڧڧܧӧ, ާ ߧ ?? ۧާ?ߧڧ է֧ݧ֧? ӧ ?ݧ .
  • 18. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 5 . ֧? ?էӧߧ? ٧? ֧էѧԧӧѧ ӧߧ ? ܧѧܧӧާ ? ӧڧԧݧ?.
  • 19. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 6 . ҧ?٧?ާ ?ӧ? ҧ ҧ?.
  • 20. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 7 . ܧ?ާ NEXUS ާѧ ( *.nex) .
  • 21. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 8 . ѧۧ ާ? ѧܧڧ ӧڧԧݧ ? ԧӧڧ է ѧߧѧ?٧ ٧ էާԧ PAUP
  • 22. 4. BioEdit ( ѧӧ C Tomas A. Hall ) 8 . ѧۧ ާ? ѧܧڧ ӧڧԧݧ ? ԧӧڧ է ѧߧѧ?٧ ٧ էާԧ PAUP
  • 23. 5 . PAST ( ѧӧ C Tomas A. Hall )
  • 24. ѧۧӧѧاݧڧ? ?֧ѧ: 1. Parsimony, Phylogeny and Genomics . 2005. Albert,V.A. (ed.) C Oxford Univ. Press, New York. ix + 229 p. 2. Lipscomb, D. 1998. Basics of Cladistic Analisys . G.Washington Univ., Washington, D.C. 75 p.