Fitmodel

This program provides maximum likelihood estimates of the parameters of a substitution model given a phylogenetic tree and an alignment of homologous sequences. A broad range of Markov models of nucleotides and amino acids substitutions are implemented. Coding sequences can also be analysed under various codon-based models of substitution, including those described in Guindon, Rodrigo, Dyer and Huelsenbeck (2004). These models are especially useful as they accommodate site-specific switches between selection regimes.


	Fitmodel fits substitution models to DNA or amino-acid sequence data sets using Maximum Likelihood This program provides maximum likelihood estimates of the parameters of a substitution model given a phylogenetic tree and an alignment of homologous sequences. A broad range of Markov models of nucleotides and amino acids substitutions are implemented. Coding sequences can also be analysed under various codon-based models of substitution, including those described in Guindon, Rodrigo, Dyer and Huelsenbeck (2004). These models are especially useful as they accommodate site-specific switches between selection regimes.


	Quick start The program takes as input a tree in NEWICK format and sequences in PHYLIP format. A PHYLIP-like interface allows to select a model of substitution. Results are stored in two output files. The 'fitmodel_stat' file provides maximum likelihood estimates of the parameter of the substitution model. The phylogeny with maximum likelihood branch length estimates is written in the 'fitmodel_tree' file. Please feel free to contact me if you have any comment or request.


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