Phylip??????????????

1
????????????????

• ??????
• 2004.5

2
????

• ????????
• ?????????
• Phylip??????????????
• PAUP???????????

3
????

• ????????
• ?????????
• Phylip??????????????
• PAUP???????????

4
?????????

• ????????????,???????????????????
• ???????
• ?????????????????????????????????

5
The affinities of all the beings of the same
class have sometimes be represented by a great
tree. I believe this simile largely speaks the
truth The green and budding twigs may
represent existing species and those produced
during former years may represent the long
succession of extinct species.. .the great Tree
of Life.covers the earth with ever-branching and
beautiful ramifications
??? ?????1859 131-132?
6
?????????? Willi Hennig (?????? ) 1966
7
?????????
???????????????(???,???)?
8
???????
????
??
??
??
??
????
????
??
?
9
???????????
A
B
C
D
F
G
F
G
C
D
A
B
E
E
10
????????
R
R
R
11
?????????(??)

• ????????????????????????

12
?????????(??)

• ??????????????????????,??????????????????(?????,
  1965 )

13
?????????(??)

• ????????????,?????????????????????????

14
?????
?????????????
x
? ? ? ? ?
????
15
????

• ????????
• ?????????
• Phylip??????????????
• PAUP???????????

16
???????????
?????(????,????)
??????(????)
?????
?????
17
????????????

• ???(distance)
• ?????(maximum parsimony,MP)
• ?????(maximum likelihood,ML)
• ????(????bayes)
• ??????gene order,gene content?

18
???(?)

• ??????????,?????????????,???????(??????)????????
  ??????,????????????????????????????????? ?

19
???(?)

• ????????????????,????
• 1.?????????????(UPGMA)?
• 2.????????????????????????(LS)?
• 3.???????????????????????????????????????(ME)?
• 4.????????????????????????????????????(NJ)

20
???(Neighbour-joining)

• ??????????????????????????????

A
D
B
C
?
E
?
F
?
21
NJ????

• ???????????(???????)?
• ???????????????????????
• ????
• ???
• ?????????,NJ???????????

22
?????(MP)

• ?????(maximum parsimony,MP)??????????,??????????
  ??????????????????????(Ockham)????,??????????????
  ???????????????????????????????,??????????????????
  ,??????

23
?????(MP)

• ??
• ????????????????????????????(????)?
• ??,??????????????????????????????

24
?????(MP)

• ??
• ????????????????????,???????????????,???????????
  ?????????
• ??????????????????????,?????????????????,???????
  ??????????????????????

25
??MP???
AGTTGTAGGTATGCCGA
AGTAGTACGTATGCCTA
AGTAGTACGTATGCCGA
AGTAGCACGTATGACTA
AGTAGTACGT -ATGCCTA
AGTAGTACGTATGCCGA
AGTTGTACGTATGCCGA
26
?????(ML)

• ?????(maximum likelihood,ML)????????????????????
  ????,?????????????????????????????

27
?????(ML)

• ????????,???????????????????????,???????????????
  ??????,?????????????????????????????????,?????????
  ???????????????,?????????????? ?

28
?????(ML)

• ??????????????????,???????????????,?????????????
  ??????
• ???????????????????????,????????????,??????????,
  ???????????????????????????????????,??????????????
  ???????

29
?????(ML)

• ?????????????????????,??????,???????????????????
  ?????????,??????,?????????????????????????,???????
  ?????????,????????????,???????????????

30
?????

• ???????????,?????????????????????,????????????

31
?????
???
????
???
????
32
?????

• ??????
• ?????? (??? NJ?)
• ???????????????????

33
???????

• ??
• ??????????
• ???????
• ????????????????
• ???????
• ???????????
• ??????
• ????

34
????

• Nearest-neighbour interchange (NNI)

35

• Subtree pruning and regrafting (SPR)

36

• Tree-bisection reconnection (TBR)

37
????(????bayes)

• ?????????????????????????????3??????????????????
  ????????,???????????????????????????????,?????????
  ???(???25?????)?,???????????????????(Bayesian
  method)??????????????,????????????????,???????????
  

38
????(????bayes)

• ???????????????,????????????????????????????????
  ????????,????X?Y,??Y????X?????(?pXY??)????X????
  Y?????(?pYX??)??X???(pX)???Y???(pY)????????
  ??
• pXYpXpYX/pY

39
????(????bayes)

• ?????????????????????????????????,??????????????
  ?????????????????????????????????????????,????????
  ?????
• ?????????????????????(MrBayes)

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??????-gene order

• ??????????????????????
• ??????????????????????????????
• Ref
• Sankoff D. et al. PNAS USA. 1992 Jul
  1589(14)6575-9

41
??????-gene content

• ??????????????????????
• ?????????????(???????-share gene,gene
  pairs,?????????)????????????
• Ref
• Snel B. et al. Nat Genet. 1999 Jan21(1)108-10.

42
???????????

• 1.Orthologus ? paralogous
• (?????????)
• ??????????????????
• (???)
• ????????????????????,???????????

43
paralogous
A
C
b
orthologous
orthologous
A
c
B
C
a
b
A mixture of orthologues and paralogues sampled
Duplication to give 2 copies paralogues on the
same genome
??????
Ancestral gene
??????
44
2.?????,???
Bacterium 1
Cladograms show branching order - branch lengths
are meaningless ?????,??????,??????
Bacterium 2
Bacterium 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4
Phylograms show branch order and branch
lengths ???,????????
Bacterium 1
Bacterium 2
Bacterium 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4
45
3.???,???,???
archaea
archaea
???
archaea
???
Rooted by outgroup
bacteria outgroup
archaea
Monophyletic group(???)
archaea
archaea
eukaryote
???
Monophyletic group
eukaryote
root
eukaryote
eukaryote
46
4.???,???
A
a
Species tree
Gene tree
B
b
D
c
We often assume that gene trees give us species
trees
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????

• ????????
• ?????????
• Phylip??????????????
• PAUP???????????

48
???????????

• 1.Phylip
• ????????????,???????????????,???????????
• http//evolution.genetics.washington.edu/phylip.ht
  ml
• 2. PAUP
• ????????????????????????,??????MP?,???????????
  ?ML?,???mac,win,linux?????,?????????,????????????

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Phylip?????

• Phylip??????????(phylogenetics)??????????????
• http//evolution.genetics,washington.edu/phylip.h
  tml
• ????????????,1980?????,??????3.6(2000?6?)?

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Phylip?????

• Phylip???35??????,???????????????,?????????????
  ?????????
• Phylip??????????(??windows,Macintosh,DOS,Linux,
  Unix?OpenVMX)?

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Phylip?????

• Phylip?????????????????,????????????????,?????
  ,?????,?????,???????

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Phylip???????

• ?????
• 1.?????protpars,proml,promlk,
• protdist
• 2.????dnapenny,dnapars,
• dnamove,dnaml,dnamlk,
• dnainvar,dnadist,dnacomp

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Phylip???????

• ?????
• Fitch,kitsch,neighbor
• ?????
• Gendist,contml
• ?????
• Pars,mix,move,penny,dollop,dolmove,dolpenny,clique
  ,factor

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Phylip???????

• ??????drawtree,drawgram
• ??restdist,restml,seqboot,contrast
• treedist,consense,retree

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Phylip??????

• Phylip????????????,?????????,?????????,???????
  ??????????
• ??,Phylip????????????(c??)?

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Phylip??????

• 1,????????,???????
• ?,?????DNA??,??????????????(dnapenny,dnapars,
  dnamove,dnaml,dnamlk,
  dnainvar,dnadist,dnacomp )??????????,???????
  ,??????????????

57
Phylip??????

• 2.?????????
• ??????DNA??,???????(DNAPARS),???(DNAML,
  DNAMLK),????(DNADIST)???

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Phylip??????

• 3.????
• ??????,??,??????,???????,????,???????outfile,ou
  ttree?

59
Phylip??????

• Outfile???????,???????????,??????????(????)???
• outtree?????????,???phylip???????????,??????????
  ??,?treeview

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(No Transcript)
61
????(??????????)

• ????-???????????
• ????-???(protdist.exe)
• ?????(protpars.exe)
• ?????(proml.exe)
• ????-???(bootstrap)

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????

• Phylip??????????????????????????????????,??????
  ?????????,????????????????(???)?
• ?????????clustal???????? ???????
• ???????(protdist.exe)

63

• ???????protdist.exe,?????????
• ???(?????infile)?

64

• ?????????,????,???
• ?????????outfile?
• ???????????????????(fitch.exe,kotsch.exe,neighbor
  .exe)?
• ???????????????infile,?????????(neighbor.exe)????
  ???????,??outfile?outtree???????

65
(No Transcript)
66

• ????????,outtree????????,???treeview??????outfi
  le????????????,?????????????,???????????

outtree
outfile
67
??????(bootstrap)

• ?????????????????????????????????????????????????
• 1.??????
• 2.?????????????
• 3.??????
• ?????????????????????
• ??????bootstrap???

68
Bootstrap??

• Phylip???????????bootstrap??????(seqboot.exe,conse
  nce.exe)?
• ????
• 1.Seqboot????????
• 2.???????????????????
• 3.?consence??????

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????

• ????????
• ?????????
• Phylip??????????????
• PAUP???????????

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PAUP???

• PAUP?????(Nexus)

NEXUS begin taxa dimensions ntax12 taxlabels
Lemur_catta Tarsius_syrichta end begin
characters dimensions nchar898 format
missing? gap- matchchar. interleave
datatypedna options gapmodemissing matrix L
emur_catta AAGCTTCATAGGAGCAACCATTCTAATAATCGC
ACATGGCCTTACATCATCCATATTATT Homo_sapiens
AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCT
CATTACTATT Pan
AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCT
CATTATTATT Gorilla
AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCAT
CATTATTATT Pongo AAGCTTCACCGGCGCAACC
ACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTT Hylobate
s AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGA
CTAACCTCTTCCCTGCTATT
71

• begin assumptions
• charset coding 2-457 660-896
• charset noncoding 1 458-659 897-898
• charset 1stpos 2-457\3 660-896\3
• charset 2ndpos 3-457\3 661-896\3
• charset 3rdpos 4-457\3 662-.\3
• exset coding noncoding
• exset noncoding coding
• usertype 2_1 4 weights transversions 2 times
  transitions
• a c g t
• a . 2 1 2
• c 2 . 2 1
• g 1 2 . 2
• t 2 1 2 .
• usertype 3_1 4 weights transversions 3 times
  transitions

72

• PAUP?????(Nexus)
• ????taxa,characters,assumptions,sets,trees,codo
  ns,distances,paup??????
• ?????????,taxa,characters????????????????????(
  mac),??????(win,linux),????nexus?????paup???

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PAUP?Nexus????

• 1.TAXA?
• ???????????(?????)??,?????????(?????)?
• 2. CHARACTERS ?
• ?????????(????????)??????????(??????,???????)

74

• 3. ASSUMPTIONS?
• ???????????,????????????,????gap??????,??????
  ?????????,??????????
• 4. SETS?
• ??????????,?????,????,????????????????

75

• 5. TREES ?
• ???????????????????,????????
• 6. CODONS ?
• ????????????????????(??????,???????)?
• 7. DISTANCES ?
• ??????????

76

• 8. PAUP ?
• ???????,??????????????(90????)???????
• ????????????????,???????????(???),?????????????
  ????????(????dos??????)???????????????? ,???????
• ??????????????,??????????????????????????????
  ???????????

77
??PAUP???????

• 1.??clustalw/clustalx???????????(?????????,???bioe
  dit??????)????nexus?????,??????????????nexus???pau
  p?????tonexus?????????(??phylip,GCG???)??????nexu
  s??????

78

• 2.?PAUP???????(Nexus??)

?????????
???????
???????
????????????? ??????????????,???????????????????ne
xus??,???????,????????????
79

• 3.??????,????
• ????????
• ????????
• ?? ??????????

80
??(???)

• 1.????
• ???????(????????)
• ??log start file your_log_file_name
• ??log stop

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??(???)

• 2.????
• ???????
• ?include coding/only
• exclude coding/only
• ???????(?????)?
• ? delete 1 ?? delete taxa_name
• undelete 1

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??(???)

• 3.??????
• ???????????? ????
• ??Set criterionparsimonylikelihooddistance

83
?? (???)

• 4.??????
• Set ??????????,???????????
• ?set maxtree10000 increaseno autocloseyes

84
?? (???)

• 5.??????(????????)
• ???alltrees
• ??????bandb
• ?????hsearch
• ??puzzle(??likelihood???)

85
?? (???)

• 6.???????(???????????)
• ???dset
• ?dset distancetamnei negbrlenallow
• ?????pset
• ? pset collapseno gapmodenewstate
• ?????lset
• ?lset nst6 clockyes

86
?? (???)

• 7.??????
• ????????(outgroup)?
• ? outgroup 1,2 ?? outgroup taxa_set
• ?????

87
?? (???)

• 7.?????
• ???NJ,UPGMA
• ?????,?????
• Hsearch ?????????
• ?hsearch andseqrandom swapspr

88
??(????)

• 8.??????
• ???????
• Bootstrap(???)
• ????,??????????????,??????,???,?????????????????
  ???????????????????,???????????????????,??????????
  ???

89
?? (????)
???bootstrap??
Bootstrap???
90
?? (????)
PAUP??bootstrap??

• BOOTSTRAP options/heuristic-search-optionsbran
  ch-and-bound-search-options
• ???????????????????bootstrap???
• ??
• BSEED integer-value ??????
• NREPS integer-value bootstrap?????,????100?
• SEARCH HEURISTICBANDBFASTSTEPNJUPGMA ????
• CONLEVEL integer-value bootstrap?????????,???
  50?
• KEEPALL YESNO
• WTS IGNORESIMPLEREPEATCNTPROPORTIONAL
• NCHAR CURRENTnumber-of-characters ??????????
• GRPFREQ YESNO ??bootstrap????
• TREEFILE bootstrap-tree-file-name ????
• FORMAT NEXUSALTNEXUSFREQPARSPHYLIPHENNIG
• BRLENS YESNO ?????
• REPLACE YESNO
• CUTOFFPCT integer-value ???????bootstrap?????
• Example
• bootstrap nreps200 treefileboot.tre
  searchheuristic/addseqrandom

91
?? (????)

• ????(jackknife)
• ?bootstrap??,???????????????????????????????????
  ???????????????????
• ??????????bootstrap?????
• ????????,???bootstrap????

92
?? (????)
PAUP??jackknife??

• JACKKNIFE options/heuristic-search-optionsbran
  chand-bound-search-options ????
• PCTDELETE real-value ????????????data
  set???
• JSEED integer-value ?????
• NREPS integer-value ??????
• SEARCH HEURISTICBANDBFASTSTEPNJUPGMA
  ??????(NJ?UPGMA?????
• ??distance????)
• RESAMPLE NORMALJAC
• CONLEVEL integer-value boostrap????????(????
  group),???50,?50
• KEEPALL YESNO ??conlevel??,???????,???
• WTS IGNORESIMPLEREPEATCNTPROPORTIONAL
• GRPFREQ YESNO ????????
• TREEFILE tree-file-name
• FORMAT NEXUSALTNEXUSFREQPARSPHYLIPHENNIG
• REPLACE YESNO
• CUTOFFPCT integer-value ??????????????
• Example
• JACKKNIFE nreps200 treefiletree.tre
  searchheuristic/addseqrandom

93
?? (????)

• KHtest?SHtest
• ?????????????ml??mp?????????????????????(?????
  Hypothesis test)?
• PAUP?????????pscores?lscores?????,????,?????
  ???????,???????
• Pscore??KHtest,???SHtest
• Lscore??KHtest?SHtest

94
?? (????)

• ?
• Pscores all/khtestnormal
• Lscores all/khtest normal shtestrell
• ???????????????????(P?)?

95
?? (????)

• ????
• ????permute
• ?????????? hompart

96
??????

• 1.??????
• Savetrees
• ???????????????
• ?savetrees filetree.tre brlensyes
  savebootpboth from1 to2
• 2.??????
• Log stop

97
??

• 3.??????????,?????????????????
• ??factory ??????????
• 4.??????
• ?? quit

98
???????

• 1.Treeinfo
• ?????????(???????????)?
• 2.clear
• ??????????
• 3.showtree
• ???????(????????,??????)
• ?showtree allshowtree 2,3
• 4.gettrees
• ????????????

99

• 5.dscores,pscores,lscores
• ??????,???,??????
• 6.ingroup/outgroup
• ????????
• 7.Contree
• ????????????
• 8.Deroottrees
• ??????????
• 9.Roottrees
• ???????outgroup??????????

100

• 10.Filter
• ???????????
• 11.????????paup???command reference?

101
Paup??????

• begin paup
• Log star filelog.txt
• set criterionlikelihood autocloseyes
  maxtrees10000 increaseno
• lset nst6 rmatrixestimate basefreqestimate
  pinvestimate ratesgamma shapeestimate
• hsearch addseqrandom nreps100
• bootstrap nreps1000 searchheuristic
  brlensyes
• savetrees filetree.tre savebootpboth
  from1 to1
• log stop
• quit
• end

102

• url
• http//life.zsu.edu.cn/bioinformatics/2004_05_phyl
  ogenesis.pps
• ????!
• ????,???
• yuansen_huang_at_hotmail.com