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Presentation by |
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Jacqueline Cantwell Jonathan Danieley |
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Song Xiang |
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General description of PHYLIP |
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What the programs do |
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Overview of the input and output formats |
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The Algorithm for Constructing Trees |
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Strategy for Finding the Best Tree |
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Relative Speed of Different Programs |
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Sample runs of the programs |
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Other phylogeny programs available elsewhere |
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Free package of 30 programs |
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-http://evolution.genetics.washington.edu/phylip.htm |
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Programs infer phylogenies |
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Able to work with different types of data |
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Molecular sequence data |
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Distance matrix data |
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Gene frequencies and continuous characters |
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Discrete state data (0|1) |
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Plotting trees and consensus trees |
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PROTPARS |
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DNAMOVE |
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DNACOMP |
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DNAML |
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RESTML |
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DNAPARS |
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DNAPENNY |
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DNAINVAR |
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DNAMLK |
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PROTDIST |
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MIX |
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MOVE |
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PENNY |
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DOLLOP, DOLMOVE, DOLPENNY |
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CLIQUE |
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FACTOR |
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DRAWGRAM |
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DRAWTREE |
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CONSENSE |
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RETREE |
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File name “infile” |
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1st line |
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#of species
#characters in free format |
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Information for each species |
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Name (length 10 ) |
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Data
(separate by spaces) |
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single letter or digit |
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Real numbers with decimal points |
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2 file output |
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“outfile”
“treefile” |
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“outfile” |
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Name of program used and version # |
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Input information printed out (from in file) |
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Series of phylogenies |
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Info on how much change on each part of the tree |
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((Mouse,Bovine),((Orang,(Gorilla,(Chimp,Human))),Gibbon)); |
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((cat:47.14069,(weasel:18.87953,((dog:25.46154,(raccoon:19.19959, |
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bear:6.80041):0.84600):3.87382,(sea_lion:11.99700, |
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seal:12.00300):7.52973):2.09461):20.59201):25.0,monkey:75.85931); |
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Input to tree drawing programs |
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Use Jumble option to randomize input order |
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Random number 4n+1 |
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Many times (10) |
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Use Global arrangement if available |
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For single runs |
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Species causing confusion last in input order |
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Do many runs adjusting ordering |
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Minimize or Maximize some quality |
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Do not search all topologies |
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Algorithm: |
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First 2 or 3 entries |
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Create tree (1 possible topology) |
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Add one entry finding best bifurcating tree |
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Local Rearrangement |
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Global Rearrangement(optional) |
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O(n2) Neighbor |
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O(n3) sequential adding |
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O(n4) Fitch, Kitsch |
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NP-complete
…Penny,Clique |
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Notes