Add phylip distance matrix as output

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.

To build, you need to use cmake. Type

git clone https://github.com/veg/tn93.git
cd tn93
cmake .
make install

Note, you can use :

cmake [-DCMAKE_INSTALL_PREFIX=/install/path DEFAULT /usr/local/] ./

to set a different install path.

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]]
}

DEPENDENCIES

gcc >= 5.0.0
cmake >= 3.0.0

ARGUMENTS

optional arguments:
  -h, --help               show this help message and exit
  -v, --version            show tn93 version 
  -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);
  -g FRACTION              in combination with AMBIGS, works to limit (for resolve and string options to AMBIG)
                           the maximum tolerated FRACTION of ambiguous characters; sequences whose pairwise comparisons
                           include no more than FRACTION [0,1] of sites with resolvable ambiguities will be resolved
                           while all others will be AVERAGED (default=1.0)
  -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 file
  -r                       if -b is specified AND -s is supplied, using -r will bootstrap across sites
                           instead of allocating sequences to 'compartments' randomly
  -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) 
  -0                       report distances between each sequence and itself (as 0); this is useful to ensure every sequence
                           in the input file appears in the output, e.g. for network construction to contrast clustered/unclustered
  -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.

	for (; p + 2 <= span_start; p+=2) {
	unsigned c1 = s1[p], c2 = s2[p];
	unsigned c3 = s1[p+1], c4 = s2[p+1];

	if (__builtin_expect(c1 < 4 && c2 < 4, 1)) {
	integer_counts [c1][c2] ++;
	} else { // not both resolved
	if (c1 == GAP \|\| c2 == GAP) {
	continue;
	}
	ambiguityHandler (c1,c2);
	}

	if (__builtin_expect(c3 < 4 && c4 < 4, 1)) {
	integer_counts2 [c3][c4] ++;
	} else { // not both resolved
	if (c3 == GAP \|\| c4 == GAP) {
	continue;
	}
	ambiguityHandler (c3,c4);
	}
	}

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TN93

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