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PAML: Phylogenetic Analysis by Maximum Likelihood

PAML: Phylogenetic Analysis by Maximum Likelihood. http://abacus.gene.ucl.ac.uk/ http://abacus.gene.ucl.ac.uk/software/paml.html. PAML programs. PAML Documentation. doc in doc/: pamlDOC.pdf, pamlFAQ.pdf, pamlHistory.txt examples/ are provided with README files

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PAML: Phylogenetic Analysis by Maximum Likelihood

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  1. PAML:Phylogenetic Analysis by Maximum Likelihood http://abacus.gene.ucl.ac.uk/ http://abacus.gene.ucl.ac.uk/software/paml.html

  2. PAML programs

  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_2TCATTCTATCTATCGTGATG sequence_3TCATTCTATCTATCGTGATG sequence_4TCATTCTATCTATCGTGATG

  7. PAML also accepts simple nexus format, with no comments.

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