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                           Version 1.0
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                           Introduction
This stand-alone software is designed to reliably detect recent positive
selection in a varying size population, even if you only have polymorphism
data from a single locus (i.e. a very short piece of DNA). The method 
itself has been described in Li (2011).

In the paper, we have proved that the MFDM test is free from the confounding
signatures of demography, including population size expansion, bottleneck and
population structure. As you may know, it's always difficult to exclude the
confounding effects of demography completely when detecting recent positive
selection, even if genome-wide polymorphism data is considered. Thus, we hope
the software would help you to address whether your targeted nuclear genes are 
affected by recent positive selection or not. The logic behind this approach is:
by examining tree topology, we can distinguish selection from varying population
size. By using a simple sampling strategy (when your samples do not cover the
whole species range), we can remove the confounding effect of population structure.
That's why genome-wide polymorphism data is not always necessary here. However,
when multiple-locus data are available, it does improve the power of detecting
selection. So in the future, we are expecting to release a new version of software
implementing an extended multiple-locus test. In the next versions, we will also
provide you a friendly user interface.

Note: The MFDM requires the beneficial allele and the sequenced locus are partially
linked. So if there is no evidence of recombination on mitochondria, 
this method may not be suitable for detecting selection on mitochondria.

If you have questions, please contact Yuting Wang (wangyuting@picb.ac.cn) or 
Haipeng Li (lihaipeng@picb.ac.cn).

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                            Installation
1. Unzip the MFDM_1.0.zip file and you will get four files:
MFDMCommandLine_1.0.jar, configFile.txt, MFDM_readMe.txt and testFile folder.

2. MFDM requires Java 2 Standard Edition (J2SE) 6 or higher, only the Java 
Runtime Environment (JRE) is required. You can visit the web: 
http://www.oracle.com/technetwork/java/javase/downloads/index.html

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                      Input file requirements
The MFDM program could process DNA files of standard fasta format
(the suffix should be .fa or .fasta, case insensitive). It can analyze
single fasta file or multiple fasta files under a common directory
(MFDM will recursively traverse the directory and pick fasta files out).
For a single fasta file, it must be aligned first and contains samples and
at least one outgroup.

* Note: If your sample size is n, the minimum significance level you can reach is 2/(n-1).
* Note: Assuming your sampling locations do not cover the whole species distribution
area, and these uncovered areas are separated into several isolated regions due to 
natural barriers. Then try to collect one individual/chromosome from each isolated 
(and uncovered) regions. Those individuals will be used as migrant detectors. Usually, 
2 or 5 migrant detectors should be enough.

MFDM could analyze 3 types of DNA sequences: phased haplotype; unphased haplotype and
diplotype. Below are 3 examples of these data types, where n = 6.

Phased haplotype (Recommended!!! MFDM only consider MD and calculate minimum number of 
recombination events for this file type.):
>Hap1
GTGCGCGGAGGCGA
>Hap2
TTGCGCGGAGGGGA
>Hap3
GTGCGCGGAGGCGA
>Hap4
TTGCGCGGAGGCGC
>Hap5
TTGCGCGGAGGCGA
>Hap6
TTGCGCGGAGGGGC

Unphased haplotype:
>Ind1_a
GTGCGCGGAGGGGA
>Ind1_b
TTGCGCGGAGGCGA
>Ind2_a
GTGCGCGGAGGCGA
>Ind2_b
TTGCGCGGAGGCGC
>Ind3_a
TTGCGCGGAGGGGA
>Ind3_b
TTGCGCGGAGGCGC

Diplotype:
>Ind1
KTGCGCGGAGGSGA
>Ind2
KTGCGCGGAGGCGM
>Ind3
TTGCGCGGAGGSGM

A  adenosine          C  cytidine             G  guanine
T  thymidine          N  A/G/C/T (any)        U  uridine 
K  G/T (keto)         S  G/C (strong)         Y  T/C (pyrimidine) 
M  A/C (amino)        W  A/T (weak)           R  G/A (purine)        
B  G/T/C              D  G/A/T                H  A/C/T      
V  G/C/A              -  gap of indeterminate length

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                               Usage
To run the project from the command line, go to the specific folder containing
MFDMCommandLine_1.0.jar and configFile.txt and type the following:

java -jar "MFDMCommandLine_1.0.jar" configFile.txt

* Note: DO NOT change the format of configFile.txt !!!
        You could change the corresponding value below a prompt according to your usage.
        If the program runs well, you will get your results file in the current directory
        (where you start the program) (default).

If you do not want to use configFile.txt or the configFile.txt does not exist,
you can simply type the following:

java -jar "MFDMCommandLine_1.0.jar"

Then follow the prompt to type corresponding parameters. 
* Note: If some prompt says that "...(default value)", you can simply skip the input 
        process by pressing ENTER key. And you could use the testFiles to test MFDM!

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                             References
Li H. A new test for detecting recent positive selection that is free from
the confounding impacts of demography. Mol.Biol.Evol. 2011; 28:365-375.
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