im
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
im [2007/12/06 10:35] – heidi | im [2011/07/14 14:26] (current) – heidi | ||
---|---|---|---|
Line 2: | Line 2: | ||
{{im.jpg? | {{im.jpg? | ||
- | **[[http://lifesci.rutgers.edu/ | + | **[[http://genfaculty.rutgers.edu/ |
- | [[http:// | + | [[http:// |
\\ | \\ | ||
- | updated | + | updated |
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, | 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, | ||
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 | ||
+ | |||
===== Program information ===== | ===== Program information ===== | ||
- | * written in C | + | * written in C++ |
* unix/linux | * unix/linux | ||
* dos/windows | * dos/windows | ||
* Mac | * Mac | ||
+ | |||
+ | |||
+ | |||
===== Data type handled ===== | ===== Data type handled ===== | ||
+ | * DNA | ||
+ | * Microsatellites (STR) | ||
+ | |||
+ | |||
Line 45: | Line 53: | ||
* 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 | ||
+ | |||
+ | |||
==== example: ==== | ==== example: ==== | ||
Line 54: | Line 64: | ||
3 | 3 | ||
locus1 1 1 13 I 1 0.0000000008 (0.0000000001, | locus1 1 1 13 I 1 0.0000000008 (0.0000000001, | ||
- | pop1_1 ACTACTGTCATGA | + | pop1_1 |
- | pop2_1 AGTACTATCACGA | + | pop2_1 |
hapstrexample 2 1 4 J2 0.75 | hapstrexample 2 1 4 J2 0.75 | ||
- | pop1_1 13 34 GTAC | + | pop1_1 |
- | pop1_2 12 35 GTAT | + | pop1_2 |
- | pop2_1 12 37 GTAT | + | pop2_1 |
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 | ||
Line 67: | Line 77: | ||
</ | </ | ||
+ | |||
===== 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): | ||
+ | * 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): |
im.1196933700.txt.gz · Last modified: 2008/07/22 13:30 (external edit)