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altree: Analysing phylogeny trees

altree - Analysing phylogeny trees
altree [options] Options: --version program version --short-help|h brief help message --help help message with options descriptions --man full documentation --association|a perform the association test --s-localisation|l perform the localisation using the S character --first-input-file|i result_file from phylogeny reconstruction programs --second-input-file|j file containing the nb of cases/controls carrying an haplotype --output-file|o output_file --data-type|t DNA|SNP --outgroup outgroup_name --remove-outgroup --tree-building-program|p phylip|paup|paml --splitmode|s nosplit|chi2split --prolongation|b --chi2-threshold|n value --permutations|r number --number-of-trees-to-analyse number --tree-to-analyse number --s-site-number number --s-site-characters ancestral state -> derived state --co-evo|e simple|double --print-tree --anc-seq ancestral sequence (only with phylip)


--version Print the program version and exits. --short-help Print a brief help message and exits. --help Print a help message with options descriptions and exits. --man Prints the manual page and exits. --association|a Perform the association test --s-localisation|l Localise the susceptibility locus using the "S-character method" --first-input-file|i result_file Input file 1 (paup, phylip or paml results file) --second-input-file|j correspond_file Input file 2, default correspond.txt --output-file|o outfile Output file --data-type|t "DNA"|"SNP" Type of data: DNA (ATGCU) or SNP (0-1) --outgroup "outgroup" Root the tree with this outgroup --remove-outgroup Remove the outgroup of the tree before performing the tests --tree-building-program|p "phylip"|"paup"|"paml" Phylogeny reconstruction program --splitmode|s "nosplit"|"chi2split" how tests are performed from a level to another --prolongation|b Prolongation of branches in the tree --chi2-threshold|n value Significance threshold for chi2 (default value 0.01) --permutations|r number Number of permutations used to calculate exact p_values (Only for association test) --number-of-trees-to-analyse number Number of trees to analyse in the localisation analysis (only for localisation method using S-character) --tree-to-analyse number With this option, you can specify the tree to use (instead of random). Can be used several times to specify multiple trees. --s-site-number number Number of the S character site in the sequence (only for localisation method using S-character) s-site-characters Character states for the S character: ancestral state -> derived state ex: G->C or 0->1 (only for localisation method using S-character) co-evo|e Type of co-evolution indice simple: only the anc -> der transition of S is used double: the two possible transitions are used print-tree If this option is selected, the tree will be printed to the output anc-seq With this option, you can specify the ancestral sequence. This option is only useful when the tree is reconstructed using the mix program of phylip with the ancestral states specified in the file "ancestors"


This program will read the given input file(s) and do someting useful with the contents thereof. ALTREE(1)

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