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PHYLIP #

PHYLIP은 the PHYLogeny Inference Package의 약자로 DNA나 Protein 서열을 이용한 계통분류 분석 프로그램을 모아놓은 패키지이다. 각 프로그램은 command line(shell, terminal, cmd)에서 실행되는 프로그램이며, 프로그램을 실행하는 디렉토리에 입력 파일이 infile 이라는 이름으로 존재해야 한다. 그렇지 않으면 프로그램 실행시 infile을 찾지 못해서 입력 파일로 사용할 파일의 이름을 입력하는 단계를 거쳐야 한다. 그리고 계산에 필요한 옵션들을 지정하는 메뉴가 나타나고 분석을 실행하면, outfile 또는 outtree 등의 이름으로 결과 파일이 생성된다.

계통분류분석 #

일반적으로 PHYLIP을 이용하여 계통분류분석을 하고자 할 때 다음과 같은 과정을 거치며 각 단계마다 사용되는 프로그램은 아래와 같다.

  1. muliple alignment : clustalw, muscle등
  2. Distance matrix 계산 : DNADIST 또는 PROTDIST
  3. Tree 데이터 작성 : Neighbor
  4. Tree 가시화 : drawtree, TreeView

구성 프로그램 #

Molecular sequence methods #

Program Documentation
protpars protein parsimony documentation file
dnapars DNA sequence parsimony documentation file
dnapenny DNA parsimony branch and bound documentation file
dnamove interactive DNA parsimony documentation file
dnacomp DNA compatibility documentation file
dnaml DNA maximum likelihood documentation file
dnamlk DNA maximum likelihood with clock documentation file
proml Protein sequence maximum likelihood documentation file
promlk Protein sequence maximum likelihood with clock documentation file
dnainvar DNA invariants documentation file
dnadist DNA distance documentation file
protdist Protein sequence distance documentation file
restdist Restriction sites and fragments distances documentation file
restml Restriction sites maximum likelihood documentation file
seqboot Bootstrapping/Jackknifing documentation file

Distance matrix methods #

Program Documentation
fitch Fitch-Margoliash distance matrix method documentation file
kitsch Fitch-Margoliash distance matrix with clock documentation file
neighbor Neighbor-Joining and UPGMA method documentation file

Gene frequencies and continuous characters #

Program Documentation
contml Maximum likelihood continuous characters and gene frequencies documentation file
contrast Contrast method documentation file
gendist Genetic distance documentation file

Discrete characters methods #

Program Documentation
pars Unordered multistate parsimony documentation file
mix Mixed method parsimony documentation file
penny Branch and bound mixed method parsimony documentation file
move Interactive mixed method parsimony documentation file
dollop Dollo and polymorphism parsimony documentation file
dolpenny Dollo and polymorphism branch and bound parsimony documentation file
dolmove Dollo and polymorphism interactive parsimony documentation file
clique 0/1 characters compatibility method documentation file
factor Character recoding program documentation file

Tree drawing, consensus, tree editing, tree distances #

Program Documentation
drawgram Rooted tree drawing program documentation file
drawtree Unrooted tree drawing program documentation file
consense Consensus tree program documentation file
treedist Tree distance program documentation file
retree interactive tree rearrangement program documentation file

참조 #

0.0.1_20240318_1_v95