PhylogenyInferencePackage, PhylogeneticTree등의 계통학적분류 프로그램 패키지.

http://evolution.genetics.washington.edu/phylip.html

It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likehood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices. It can handle data that are nucleotide sequences, protein sequence, gene frequencies, restriction sites, restriction fragments, distances, discrite characters, and continuous characters.

ClustalW등의 프로그램에서 만들어낸 파일을 이용해서, 계통도 dendrogram을 그린다.

프로그램구성

• Molecular sequence methods
  1. protpars : Protein parsimony
  2. dnapars : DNA sequence parsimony
  3. dnapenny : DNA parsimony branch and bound
  4. dnamove : interactive DNA parsimony
  5. dnacomp : DNA compatibility

  6. dnaml : DNA MaximumLikelihood

  7. dnamlk : DNA MaximumLikelihood with clock

  8. proml : Protein sequence MaximumLikelihood

  9. promlk : Protein sequence MaximumLikelihood with clock

  10. dnainvar : DNA invariants
  11. dnadist : DNA distance
  12. protdist : protein sequence distance
  13. restdist : restriction sites and fragments distances
  14. seqboot : Bootstrapping/Jackknifing
• Distance matrix methods

  1. fitch : FitchMargoliashDistanceMatrix method

  2. kitsch : FitchMargoliashDistanceMatrix with clock

  3. neighbor : NeighborJoiningMethod and [UPGMA] method

• Gene frequencies and continuous characters

  1. contml : MaximumLikelihood continuous characters and gene frequencies

  2. contrast : Contrast method
  3. gendist : Genetic distance
• Discrete characters methods
  1. pars : Unorderd multistate parsimony
  2. mix : Mixed method parsimony
  3. penny : Branch and bound mixed method parsimony
  4. move : Interactive mixed method parsimony
  5. dollop : Dollo and polymorphism parsimony
  6. dolpenny : Dollo and polymorphism branch and bound parsimony
  7. dolmove : Dollo and polymorphism interactive parsimony
  8. clique : 0/1 characters compatibility method
  9. factor : Character recoding program
• Tree drawing, consessus, tree editing, tree distances
  1. drawgram : Rooted tree drawing
  2. drawtree : Unrooted tree drawing
  3. consense : Consensus tree
  4. treeedist : Tree distance
  5. retree : interative tree rearrangement

Tree draw용 입력파일예제

((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,
seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,
weasel:18.87953):2.09460):3.87382,dog:25.46154);

(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,
Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);

(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,
(P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,
Rodent:1.21460);

CategoryProgramBio