Differences

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--- im [2007/12/06 10:31] – heidi
+++ im [2011/07/14 14:26] (current) – heidi
@@ Line 2: / Line 2: @@
 {{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]]
 \\
-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\\
 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
 ===== Program information =====
-  * written in C
+  * written in C++
   * unix/linux
   * dos/windows
   * Mac
-===== Data type handled =====
+===== Data type handled =====
+  * DNA
+  * Microsatellites (STR)
-===== Input Files =====
-contains the data for all loci to be considered
-==== example ====
-example for a tiny three locus data set. The mutation rate per year is known and specified for locus 1, but not for loci 2 and 3:
-<code>
-Example data for IM
-# im test data
-population1 population2
-locus1 1 1 13 I 1 0.0000000008 (0.0000000001, 0.0000000015)
-pop1_1 ACTACTGTCATGA
-pop2_1 AGTACTATCACGA
-hapstrexample 2 1 4 J2 0.75
-pop1_1 13 34 GTAC
-pop1_2 12 35 GTAT
-pop2_1 12 37 GTAT
-strexample 2 2 1 S1 1 0.00001 (0.000001, 0.00005)
-strpop11a 23
-strpop11b 26
-strpop21a 25
-strpop21b 31
-</code>
+===== Input Files =====
+contains the data for all loci to be considered
   * line 1 - arbitrary text, usually explaining the content of the file
@@ Line 69: / Line 54: @@
   * last line - should end with a newline so that the file ends on a blank line
+==== example: ====
+example for a tiny three locus data set. The mutation rate per year is known and specified for locus 1, but not for loci 2 and 3
+<code>
+Example data for IM
+# im test data
+population1 population2
+locus1 1 1 13 I 1 0.0000000008 (0.0000000001, 0.0000000015)
+pop1_1    ACTACTGTCATGA
+pop2_1    AGTACTATCACGA
+hapstrexample 2 1 4 J2 0.75
+pop1_1    13 34 GTAC
+pop1_2    12 35 GTAT
+pop2_1    12 37 GTAT
+strexample 2 2 1 S1 1 0.00001 (0.000001, 0.00005)
+strpop11a 23
+strpop11b 26
+strpop21a 25
+strpop21b 31
+</code>
 ===== 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.