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 INDELible Download Report Bug Tutorial Manual byWillFletcher ```///////////////////////////////////////////////////////////////////////////////////// // // // INDELible V1.03 control file - indels.txt // // // // Adding indels to a nucleotide, amino-acid or codon substitution model // // // ///////////////////////////////////////////////////////////////////////////////////// [TYPE] AMINOACID 2 // amino-acid simulation using algorithm from method 2 [MODEL] mymodel1 // this is identical to mymodel2 [submodel] WAG [insertmodel] POW 1.7 500 // Power law insertion length distribution (a=1.7, M=500) [deletemodel] POW 1.7 500 // Power law deletion length distribution (a=1.7, M=500) [insertrate] 0.1 // insertion rate = 0.1 relative to substitution rate of 1 [deleterate] 0.1 // deletion rate = 0.1 relative to substitution rate of 1 [MODEL] mymodel2 // this is identical to mymodel1 [submodel] WAG [indelmodel] POW 1.7 500 // Power law insertion/deletion length distribution (a=1.7) [indelrate] 0.1 // insertion rate = deletion rate = 0.1 // relative to average substitution rate of 1. [MODEL] mymodel3 // insertion/deletion lengths and rates can be different. [submodel] WAG [insertmodel] NB 0.2 4 // Pascal insertion length distribution (q=0.2, r=4) [deletemodel] LAV 1.8 500 // Lavalette deletion length distribution (a=1.8, M=500) [insertrate] 0.1 // insertion rate = 0.1 relative to substitution rate of 1 [deleterate] 0.2 // deletion rate = 0.2 relative to substitution rate of 1 [MODEL] mymodel4 // insertion/deletion lengths and rates can be different. [submodel] JTT [insertmodel] NB 0.4 1 // Geometric insertion length distribution (q=0.4, r=1) [insertrate] 0.1 // insertion rate = 0.1 relative to substitution rate of 1 // deletion rate = 0 relative to substitution rate of 1 [TREE] t1 (A:0.1,B:0.1); [PARTITIONS] Pname1 [t1 mymodel1 1000] // tree t1, model mymodel1, root length 1000 [PARTITIONS] Pname2 [t1 mymodel2 1000] // tree t1, model mymodel2, root length 1000 [PARTITIONS] Pname3 [t1 mymodel3 1000] // tree t1, model mymodel3, root length 1000 [PARTITIONS] Pname4 [t1 mymodel4 1000] // tree t1, model mymodel4, root length 1000 [EVOLVE] Pname1 10 outputname1 // 10 replicates generated from partition Pname1 Pname2 10 outputname2 // 10 replicates generated from partition Pname2 Pname3 10 outputname3 // 10 replicates generated from partition Pname3 Pname4 10 outputname4 // 10 replicates generated from partition Pname4 ///////////////////////////////////////////////////////////////////////////////////// /* New commands that are relevant to insertions and deletions (indels) are: [insertrate] Sets the rate of insertion relative to an average substitution rate of 1. [deleterate] Sets the rate of insertion relative to an average substitution rate of 1. [indelrate] Sets the rate of insertion AND deletion to be equal. It is equivalent to specifying [insertrate] and [deleterate] to have the same value. If [insertrate] & [indelrate] are not specified then rate of insertion is zero. If [deleterate] & [indelrate] are not specified then rate of deletion is zero. [insertmodel] Works the same as [indelmodel] but only sets the insertion length distribution. [deletemodel] Works the same as [indelmodel] but only sets the deletion length distribution. [indelmodel] This sets the insertion and deletion length distributions at the same time. It is equivalent to specifying the commands [insertmodel] and [deletemodel] to have the same value. Options for this command are: (1) [indelmodel] NB q r // Negative Binomial Distribution (2a) [indelmodel] POW a // Zipfian Distribution (2b) [indelmodel] POW a M // Zipfian Distribution (3) [indelmodel] LAV a M // Lavalette Distribution (4) [indelmodel] USER mylengthmodel.txt // User-Defined Distribution (1) This specifies a Pascal (negative binomial) distribution where q is a decimal (0<=q<=1) and r is an integer (r>0). (2a) This specifies a Zipfian (power law) distribution where a is a decimal (a>1). (2b) This also specifies a Zipfian distribution where a is a decimal (a>1). However with this format indels longer than length M are not permitted. This format is highly recommended for small values of a because of the fat-tailed shape of the resulting distribution. (3) This specifies a Lavalette distribution where a is a decimal (a>1) and M is an integer (M>1) representing the maximum indel length. (4) This specifies a user-defined indel length model. The file mylengthmodel.txt should be in the same directory as the INDELible executable and contain a list of relative frequencies (in order of increasing indel length) separated by white space, like this. */ ``` Please click here to return to the tutorial menu page for more examples.