PAML: Phylogenetic Analysis by Maximum Likelihood

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PAMLPhylogenetic Analysis by Maximum Likelihood
http//abacus.gene.ucl.ac.uk/ http//abacus.gene.u
cl.ac.uk/software/paml.html
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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)
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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

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Major weaknesses

• Poor tree search
• Poor user interface

Major strength

• Many likelihood models

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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

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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
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PAML also accepts simple nexus format, with no
comments.