PAML: Phylogenetic Analysis by Maximum Likelihood - PowerPoint PPT Presentation

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PAML: Phylogenetic Analysis by Maximum Likelihood

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... for amino acids (aaml) & codons (codonml) The world's best ... Codon models and detection of selection. Amino acid models. Ancestral sequence reconstruction ... – PowerPoint PPT presentation

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Title: PAML: Phylogenetic Analysis by Maximum Likelihood


1
PAMLPhylogenetic Analysis by Maximum Likelihood
http//abacus.gene.ucl.ac.uk/ http//abacus.gene.u
cl.ac.uk/software/paml.html
2
PAML programs
baseml basemlg codeml evolver yn00chi2 ML under nucleotide-based models Continuous-gamma, for bases (Yang 1993) ML for amino acids (aaml) codons (codonml) The worlds best named simulation program dN and dS estimation using YN2000?2 critical values and p values
pamp mcmctree Parsimony (Yang and Kumar 1996)Species divergence times, soft bounds, relaxed clocks (Yang Rannala 2006)
3
PAML Documentation
  • doc in doc/ pamlDOC.pdf, pamlFAQ.pdf,
    pamlHistory.txt
  • examples/ are provided with README files
  • Questions go to discussion group
    http//www.rannala.org/gsf

4
Major weaknesses
  • Poor tree search
  • Poor user interface

Major strength
  • Many likelihood models

5
What the package is being used for?
  • Codon models and detection of selection
  • Amino acid models
  • Ancestral sequence reconstruction
  • ML clock and local-clock models for dating
  • Combined analysis of multiple genes
  • Various other models

6
phylip data format
4 20 sequence_1 TCATT CTATC TATCG
TGATG sequence_2 TCATT CTATC TATCG
TGATG sequence_3 TCATT CTATC TATCG
TGATG sequence_4 TCATT CTATC TATCG TGATG 4
20 sequence_1TCATTCTATCTATCGTGATG sequence_2TCATTC
TATCTATCGTGATG sequence_3TCATTCTATCTATCGTGATG sequ
ence_4TCATTCTATCTATCGTGATG
7
PAML also accepts simple nexus format, with no
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