treefile D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\struct1h54_phyml_tree.txt
seqfile D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\FASTA1h54.txt
Modelweightsfile D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\weights2.txt
treeOutFile D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\treeoutbur.txt
outTreeFileNewick D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\tree.newick.txt
outTreeFileAncestor D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\tree.ancestor.txt
outFile_prob_joint D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\prob.joint.txt
outFile_prob_marginal D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\prob.marginal.txt
outFile_seq_joint D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\seq.joint.txt
outFile_seq_marginal D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\seq.marginal.txt
reportFile D:\\My Documents\\Josef\FastML\\Asher\\fastml_example\\report.txt
seqOutputFormat fasta
distributionName hom
boundMethod max
modelName MIX
gammaCategies 8
optimizeBrLenOnStartingTree 1

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