Masterarbeit, Heidi Lischer

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im [2007/12/06 10:58] – heidiim [2011/07/14 14:26] (current) – heidi
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 {{im.jpg?220}}\\ {{im.jpg?220}}\\
  
-**[[http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm#IM|IM]]**\\ +**[[http://genfaculty.rutgers.edu/hey/software#IMa2|IM]]**\\ 
-[[http://lifesci.rutgers.edu/~heylab/ProgramsandData/Programs/IM/Using_IM_3_5_2007.pdf|documentation]]+[[http://lifesci.rutgers.edu/~heylab/ProgramsandData/Programs/IM/Introduction_to_IM_and_IMa_3_5_2007.pdf|documentation]]
  
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-updated 10/23/2007\\+updated 17.12.2009\\
 IM is a program for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. Large numbers of loci can be studied simultaneously, and different mutation models can be used. IM estimates the divergence time and the migrations having occurred in the ancestry of two populations, which might have grown exponentially since split. Important limitations of the basic model are that it cannot account for changes in population sizes, and it cannot account for the sizes of founding populations\\ IM is a program for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. Large numbers of loci can be studied simultaneously, and different mutation models can be used. IM estimates the divergence time and the migrations having occurred in the ancestry of two populations, which might have grown exponentially since split. Important limitations of the basic model are that it cannot account for changes in population sizes, and it cannot account for the sizes of founding populations\\
 IMa also allows log likelihood ratio tests of nested demographic models. IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for IMa also allows log likelihood ratio tests of nested demographic models. IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for
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   * dos/windows   * dos/windows
   * Mac   * Mac
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   * DNA   * DNA
   * Microsatellites (STR)   * Microsatellites (STR)
-  * linked SNP and STR 
  
  
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   * Additional lines for additional loci - If there is more than one locus, then the data for locus 2 begins on line (n1+n2+5) with a line similar to line 4 presenting the basic information for locus 2. The sample names and sample sizes for locus 2 and the inheritance scalars and mutation model for locus 2 need not be the same as for locus 1   * Additional lines for additional loci - If there is more than one locus, then the data for locus 2 begins on line (n1+n2+5) with a line similar to line 4 presenting the basic information for locus 2. The sample names and sample sizes for locus 2 and the inheritance scalars and mutation model for locus 2 need not be the same as for locus 1
   * last line - should end with a newline so that the file ends on a blank line   * last line - should end with a newline so that the file ends on a blank line
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 ==== example: ==== ==== example: ====
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 3 3
 locus1 1 1 13 I 1 0.0000000008 (0.0000000001, 0.0000000015) locus1 1 1 13 I 1 0.0000000008 (0.0000000001, 0.0000000015)
-pop1_1 ACTACTGTCATGA +pop1_1    ACTACTGTCATGA 
-pop2_1 AGTACTATCACGA+pop2_1    AGTACTATCACGA
 hapstrexample 2 1 4 J2 0.75 hapstrexample 2 1 4 J2 0.75
-pop1_1 13 34 GTAC +pop1_1    13 34 GTAC 
-pop1_2 12 35 GTAT +pop1_2    12 35 GTAT 
-pop2_1 12 37 GTAT+pop2_1    12 37 GTAT
 strexample 2 2 1 S1 1 0.00001 (0.000001, 0.00005) strexample 2 2 1 S1 1 0.00001 (0.000001, 0.00005)
 strpop11a 23 strpop11a 23
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 </code> </code>
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 ===== How to cite ===== ===== How to cite =====
 +  * Nielsen R. and Wakeley J. (2001). Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158(2):885-96.
 +  * Hey J. and Nielsen R. (2007). Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA, 104(8):2785-90.
im.1196935134.txt.gz · Last modified: 2008/07/22 13:30 (external edit)