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资源说明：TN93 fast distance calculator
TN93
----
This is a simple program meant to compute pairwise distances between aligned
nucleotide sequences in sequential FASTA format using the
[Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).
To build, you need to use cmake. Type
$cmake [-DCMAKE_INSTALL_PREFIX=/install/path DEFAULT /usr/local/] ./
$make install
If the compiler supports OpenMP, the program will be built with multithreaded
support.
USAGE
-----
usage: tn93 [-h] [-o OUTPUT] [-t THRESHOLD] [-a AMBIGS] [-l OVERLAP][-d COUNTS_IN_NAME] [-f FORMAT] [-s SECOND_FASTA] [-b] [-c] [-q] [FASTA]
Try it from using the example file in 'data' by typing
tn93 -t 0.05 -o data/test.dst data/test.fas
Output (diagnostics written to stderr, histogram written to stdout so can be redirected)
Example:
Read 8 sequences of length 1320
Will perform 28 pairwise distance calculations
Progress: 100% ( 7 links found, inf evals/sec)
{
"Actual comparisons performed" :28,
"Total comparisons possible" : 28,
"Links found" : 7,
"Maximum distance" : 0.0955213,
"Mean distance" : 0.0644451,
"Histogram" : [[0.005,0],[0.01,0],[0.015,0],[0.02,0],[0.025,0],[0.03,2],[0.035,1],[0.04,0],[0.045,1],[0.05,3],[0.055,1],[0.06,2],[0.065,2],[0.07,3],[0.075,4],[0.08,3],[0.085,3],[0.09,2],[0.095,0],[0.1,1],[0.105,0],[0.11,0],[0.115,0],[0.12,0],[0.125,0],[0.13,0],[0.135,0],[0.14,0],[0.145,0],[0.15,0],[0.155,0],[0.16,0],[0.165,0],[0.17,0],[0.175,0],[0.18,0],[0.185,0],[0.19,0],[0.195,0],[0.2,0],[0.205,0],[0.21,0],[0.215,0],[0.22,0],[0.225,0],[0.23,0],[0.235,0],[0.24,0],[0.245,0],[0.25,0],[0.255,0],[0.26,0],[0.265,0],[0.27,0],[0.275,0],[0.28,0],[0.285,0],[0.29,0],[0.295,0],[0.3,0],[0.305,0],[0.31,0],[0.315,0],[0.32,0],[0.325,0],[0.33,0],[0.335,0],[0.34,0],[0.345,0],[0.35,0],[0.355,0],[0.36,0],[0.365,0],[0.37,0],[0.375,0],[0.38,0],[0.385,0],[0.39,0],[0.395,0],[0.4,0],[0.405,0],[0.41,0],[0.415,0],[0.42,0],[0.425,0],[0.43,0],[0.435,0],[0.44,0],[0.445,0],[0.45,0],[0.455,0],[0.46,0],[0.465,0],[0.47,0],[0.475,0],[0.48,0],[0.485,0],[0.49,0],[0.495,0],[0.5,0],[0.505,0],[0.51,0],[0.515,0],[0.52,0],[0.525,0],[0.53,0],[0.535,0],[0.54,0],[0.545,0],[0.55,0],[0.555,0],[0.56,0],[0.565,0],[0.57,0],[0.575,0],[0.58,0],[0.585,0],[0.59,0],[0.595,0],[0.6,0],[0.605,0],[0.61,0],[0.615,0],[0.62,0],[0.625,0],[0.63,0],[0.635,0],[0.64,0],[0.645,0],[0.65,0],[0.655,0],[0.66,0],[0.665,0],[0.67,0],[0.675,0],[0.68,0],[0.685,0],[0.69,0],[0.695,0],[0.7,0],[0.705,0],[0.71,0],[0.715,0],[0.72,0],[0.725,0],[0.73,0],[0.735,0],[0.74,0],[0.745,0],[0.75,0],[0.755,0],[0.76,0],[0.765,0],[0.77,0],[0.775,0],[0.78,0],[0.785,0],[0.79,0],[0.795,0],[0.8,0],[0.805,0],[0.81,0],[0.815,0],[0.82,0],[0.825,0],[0.83,0],[0.835,0],[0.84,0],[0.845,0],[0.85,0],[0.855,0],[0.86,0],[0.865,0],[0.87,0],[0.875,0],[0.88,0],[0.885,0],[0.89,0],[0.895,0],[0.9,0],[0.905,0],[0.91,0],[0.915,0],[0.92,0],[0.925,0],[0.93,0],[0.935,0],[0.94,0],[0.945,0],[0.95,0],[0.955,0],[0.96,0],[0.965,0],[0.97,0],[0.975,0],[0.98,0],[0.985,0],[0.99,0],[0.995,0],[1,0]]
}
ARGUMENTS
---------
optional arguments:
-h, --help show this help message and exit
-o OUTPUT direct the output to a file named OUTPUT (default=stdout)
-t THRESHOLD only report (count) distances below this threshold (>=0, default=0.015)
-a AMBIGS handle ambigous nucleotides using one of the following strategies (default=resolve)
resolve: resolve ambiguities to minimize distance (e.g.R matches A);
average: average ambiguities (e.g.R-A is 0.5 A-A and 0.5 G-A);
skip: do not include sites with ambiguous nucleotides in distance calculations;
gapmm: a gap ('-') matched to anything other than another gap is like matching an N (4-fold ambig) to it;
a string (e.g. RY): any ambiguity in the list is RESOLVED; any ambiguitiy NOT in the list is averaged (LIST-NOT LIST will also be averaged);
-f FORMAT controls the format of the output unless -c is set (default=csv)
csv: seqname1, seqname2, distance;
csvn: 1, 2, distance;
hyphy: {{d11,d12,..,d1n}...{dn1,dn2,...,dnn}}, where distances above THRESHOLD are set to 100;
-l OVERLAP only process pairs of sequences that overlap over at least OVERLAP nucleotides (an integer >0, default=100):
-d COUNTS_IN_NAME if sequence name is of the form 'somethingCOUNTS_IN_NAMEinteger' then treat the integer as a copy number
when computing distance histograms (a character, default=':'):
-s SECOND_FASTA if specified, read another FASTA file from SECOND_FASTA and perform pairwise comparison BETWEEN the files (default=NULL)
-b bootstrap alignment columns before computing distances (default = false)
when -s is supplied, permutes the assigment of sequences to files
-c only count the pairs below a threshold, do not write out all the pairs
-m compute inter- and intra-population means suitable for FST caclulations
only applied when -s is used to provide a second file -u PROBABILITY subsample sequences with specified probability (a value between 0 and 1, default = 1.0)
-q do not report progress updates and other diagnostics to stderr
FASTA read sequences to compare from this file (default=stdin)
NOTES
-----
All sequences must be aligned and have the same length. Only IUPAC characters are recognized (e.g. no ~). Sequence names can include copy number as in
>seqname:10
':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers
only affect histogram and mean calculations.
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