Detection of positively selected amino acid sites

ipssa

This module is used to automatically identify positively selected amino acid sites and check if there is evidence for recombination in the sequence data. It accepts as input one CDS FASTA file, and returns a tabular formatted file containing the results of all selected PSS methods. The parameters that must be specified in the config file for this module are: ipssa_sequence_limit (the maximum number of sequences to use for the master file. The default value is 90), ipssa_random_seed (the random seed), ipssa_align_method (the alignment method to use, one of: clustalw, muscle, kalign, t_coffee, or amap. The default value is muscle), ipssa_tcoffee_min_score (the minimum support value for alignment positions. The default value is 3), ipssa_mrbayes_generations (the number of iterations in MrBayes. The default value is 1000000), ipssa_mrbayes_burnin (the MrBayes burnin. The default value is 2500), ipssa_fubar_sequence_limit (the maximum number of sequences to be used by FUBAR. The default value is 90), ipssa_fubar_runs (the number of independent replicas for FUBAR. The default value is 1), ipssa_codeml_sequence_limit (the maximum number of sequences to be used by CodeML. The default value is 30), ipssa_codeml_runs (the number of independent replicas for CodeML. The default value is 1), ipssa_codeml_models (the CodeML models to be run, one or more of: ‘1’, ‘2’, ‘7’, and/or ‘8’. To declare more than one model use a blank space between models. The default value is 1 2 7 8), ipssa_omegamap_sequence_limit (the maximum number of sequences to be used by omegaMap. The default value is 90), ipssa_omegamap_iterations (the number of omegaMap iterations. the default value is 2500), ipssa_omegamap_runs (the number of independent replicas for omegaMap. ipssa_By default, the flag is not present and thus omegaMap is executed if ipssa_omegamap_iterations > 0). It should be noted that all parameters must be declared in the config file, even if only a subset of the available methods is to be used. In order not to use a given method, all parameters related to that method should be set to zero.