用法：
MSTMap [infile] [outfile]
infile格式:(首先是12个参数设置，然后是genotyping数据)
population_type <para1>
population_name <para2>
distance_function <para3>
cut_off_p_value <para4>
no_map_dist <para5>
no_map_size <para6>
missing_threshold <para7>
estimation_before_clustering <para8>
detect_bad_data <para9>
objective_function <para10>
number_of_loci <para11>
number_of_individual <para12>
<para1> specifies the type of mapping population being used. Possible values are DH and RILd,
where d is any natural number. For example, RIL6 means a RIL population at generation 6.
You should use DH for any population that involves only two distinct genotype states
(even if it is not a DH population), which includes BC1, DH, Hap, and advanced RIL.
<para2> gives a name for the mapping population. It can be any string of letters (a-z, A-Z)
or digits (0-9).
<para3> specifies the distance function to be used. Possible choices are kosambi and haldane,
which refers to the commonly used Kosambi's and Haldane's distance functions respectively.
<para4> specifies the threshold to be used for clustering the markers into LGs. A reasonable
choice of p_value is 0.000001. Alternatively, the user can turn off this feature by
setting <para4> to any number larger than 1. If the user does so, our software tool
assumes that all markers belong to one single linakge group.
<para5> and <para6> together allow one to detect bad markers. In high density genetic linkage
mapping, bad markers appear to be isolated from others. MSTmap will detect isolated
marker groups and will place them in seperate LGs. An isolated marker group is a
small set of markers of size less than or equal to <para6> and is more than <para5>
away from the rest of the markers. A reasonable choice for <para6> is 1 or 2. To
disable this feature, simply set <para6> to 0.
For example, if <para5>=15 and <para6>=2, then any group whose size is less than 2 and is 15
centimorgans away from the rest of the markers will be placed in a linkage group by themselves.
Occasionally there are markers with excessive number of missing observations. Those markers
can be eliminated by settting <para7> to a proper value. For example, if <para7>=0.25, then
any marker with more than 25% missing observations will be removed completely without being
mapped.
<para8> is a binary flag which can be set to yes or no. If <para8> is set to yes, then our
software tool will try to estimate missing data before clustering the markers into linkage
groups.
<para9> is a binary flag which can be set to yes or no. If <para9> is set to yes, then our
software tool will try to detect bad data during the map construction process. Those suspicious
genotype data will be printed to the console for user inspection. The error detection feature
can be turned off by setting <para9> to no.
<para10> specifies the objective function to be used. Possible choices are COUNT and ML.
COUNT refers to the commonly used sum of recombination events objective function and ML
refers to the commonly used maximum likelihood objective function.
<para11> specifies the total number of markers in the data set.
<para12> specifies the total number of mapping lines in the data set.
The body of the input file contains a table of dimension (m+1)*(n+1), where m is the total
number of markers (which is equal to the <para11> value) and n is the total number of mapping
lines (which is equal to the <para12> value). The first row gives the ids for the mapping
lines, while the first column gives the ids for the genetic markers. Each id is a string of
letters (a-z, A-Z) or digits (0-9). No space is allowed within an id. Each cell in the table
refers to the genotype state of a particular mapping line on a particular marker locus. The
genotype states can be specified with letters 'A', 'a', 'B', 'b', '-', 'U' or 'X'. 'A' and
'a' are equivalent, 'B' and 'b' are equivalent and so are '-' and 'U'. 'U' and '-' indicates
the missing genotype call. If the data set is from a RIL population, you can use 'X' to
indicate that the corresponding genotype is a heterozygous 'AB'.
