EMBOSS: distmat

| ## EMBOSS: distmat

# Program distmat

## Function

Creates a distance matrix from multiple alignments

## Description

distmat calculates the evolutionary distances between every pair of sequences in a multiple alignment. The sequences need to be aligned before running this program. The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis. This application calculates a distance matrix for the set of sequences in the alignment. The distances are expressed in terms of the number of substitutions per 100 bases or amino acids.

As sequence diverge so does the probability of there being multiple substitutions at any one site in the alignment increase. The distance will then be an underestimate of the true evolutionary distance between the sequences. Therefore, there are a number of methods for correcting the observed substitution rate for the occurence of multiple substutions.

For nucleotides, the "-position" flag allows the user to choose base positions to analyse in each codon, i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases.

### Uncorrected distances

This method does not make any corrections for multiple substitutions. Therefore, the score will be an underestimate of the distance between the sequences. This will not be less significant for highly similar sets of sequences.

    S = m/(npos + gaps*gap_penalty)                                  (1)

    m 	    - score of matches (1 for an exact match, a fraction for partial
    	      matches and 0 for no match)
    npos	    - number of positions included in m
    gaps        - number of gaps in the sequences
    gap_penalty - the score given to a gapped position

    D = uncorrected distance = p-distance = 1-S          (2)

The score of match includes all exact matches. For nucleotides, if the flag "-ambiguous" is used then partial matches are included in the score. For example, a match of M (A or C) with A will increment m by 0.5 (0.5*1.0). Gaps are not included in the calculation unless a non zero value is given with "-gapweight". It should be noted that end gaps and internal gaps will be weighted by the same amount. So it is recommended that this be used with "-sbegin"and "-send" to specify the start and end of the region to calculate the distance from.

## Multiple Substitution correction algorithms

### Jukes-Cantor

This can be used for nucleotide and protein sequences.

    distance = -b ln (1-D/b)

    D - uncorrected distance
    b - constant. b= 3/4 for nucleotides and 19/20 for proteins.

Partial matches and gap positions can be taken into account in the calculation of D, by setting the "-ambiguous" and "-gapweight" flags (see "uncorrected distance" method).

Reference:
"Phylogenetic Inference", Swofford, Olsen, Waddell, and Hillis, in Molecular Systematics, 2nd ed., Sinauer Ass., Inc., 1996, Ch. 11.

### Tajima-Nei

This method is only for nucleotide sequences. It uses the same equation as Jukes-Cantor, but the b-parameter is not constant. Also, only exact matches are considered in the calculation of the match score and gap positions are ignored.

    A = 1, T = 2, C = 3, G = 4

    b = 0.5(1.- Sum(i=A,G)(fraction[i]^2  + D^2/h)

    h = Sum(i=A,C)Sum(k=T,G) (0.5 * pair_frequency[i,k]^2/(fraction[i]*fraction[k]))

    distance = -b ln(1.-D/b)

    pair_frequency[i,k]   - frequency of the i and k base pair at sites in
    			the alignement of the pair of sequences.
    fraction[i]           - average content of the base i in both sequences

Reference:
F. Tajima and M. Nei, Mol. Biol. Evol. 1984, 1, 269.

### Kimura Two-Parameter distance

This method is only for nucleotide sequences. This uses the principle that transition substitutions (purine-purine and pyrimidine-purine) are more likely than transversion substitutions (purine-pyprimidine). Purine being the nucleic acid constituent of A and G, and pyrimidine being the nucleic acid derivative of the bases C, T and U. Gaps are ignored and abiguous symbols other than R (purine) and Y (pyrimidine) are ingnored.

    P = transitions/npos
    Q = transversions/npos

    npos - number of positions scored

    distance = -0.5 ln[ (1-2P-Q)*sqrt(1-2Q)]

Reference:
M. kimura, J. Mol. Evol. 1980, 16, 111.

### Tamura

This method is only for nucleotide sequences. This method uses transition and transversion rates and takes into account the deviation of GC content from the expected value of 50 %. Gap and ambiguous positions are ignored.

    P = transitions/npos
    Q = transversions/npos

    npos - number of positions scored

    GC1 = GC fraction in sequence 1
    GC2 = GC fraction in sequence 2
    C = GC1 + GC2 - 2*GC1*GC2

    distance = -C ln(1-P/C-Q) - 0.5(1-C) ln(1-2Q)

Reference:
K. Tamura, Mol. Biol. Evol. 1992, 9, 678.

### Jin-Nei Gamma distance

This method applies to nucleotides only. This again uses transition and transversion rates. As with the Kimura two parameter method, gaps and ambiguous symbols other than R and Y are not oncluded in the score. The shape parameter, i.e. "a", is the square of the inverse of the coefficient of variation of the average substitution,

    L = average substituition = transition_rate + 2 * transversion_rate
    a = (average L)^2/(variance of L)

    P = transitions/npos
    Q = transversions/npos

    npos - number of positions scored

    distance = 0.5 * a ((1-2P-Q)^(-1/a) + 0.5 (1-2Q)^(-1/a) -3/2)

It is suggested [Jin et al.], in general, that the distance be calculated with an a-value of 1. However, the user can specify their own value, using the "-parametera" option, or calculate for each pair of sequence, using "-calculatea".

Reference:
L. Jin and M. Nei, Mol. Biol. Evol. 1990, 7, 82.

### Kimura Protein distance

This method is used for proteins only. Gaps are ignored and only exact matches and ambiguity codes contribute to the match score.

    S = m/npos

    m  - exact match
    npos - number of positions scored

    D = 1-S
    distance = -ln(1 - D - 0.2D^2)

Reference:
M. Kimura, The Neutral Theory of Molecular Evolution, Camb. Uni. Press, Camb., 1983.

## Usage

Here is a sample session with distmat:

    % distmat pax.align
    Creates a distance matrix from multiple alignments
    Multiple substitution correction methods for proteins
             0 : Uncorrected
             1 : Jukes-Cantor
             2 : Kimura Protein
    Method to use [0]: 2
    Output file [outfile.distmat]:

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-msf]               seqset     File containing a sequence alignment.
    *  -nucmethod          menu       Multiple substitution correction methods for
                                      nucleotides.
    *  -protmethod         menu       Multiple substitution correction methods for
                                      proteins.
      [-outf]              outfile    Enter a name for the distance matrix

       Optional qualifiers (* if not always prompted):
    *  -ambiguous          bool       Option to use the abiguous codes in the
                                      calculation of the Jukes-Cantor method or if
                                      the sequences are proteins.
    *  -gapweight          float      Option to weight gaps in the uncorrected
                                      (nucleotide) and Jukes-Cantor distance
                                      methods.
    *  -position           integer    Choose base positions to analyse in each
                                      codon i.e. 123 (all bases), 12 (the first
                                      two bases), 1, 2, or 3 individual bases.
    *  -calculatea         bool       This will force the calculation of the
                                      a-parameter in the Jin-Nei Gamma distance
                                      calculation, otherwise the default is 1.0
                                      (see -parametera option).
    *  -parametera         float      User defined a parameter to be use in the
                                      Jin-Nei Gamma distance calculation. The
                                      suggested value to be used is 1.0 [Jin et
                                      al.] and this is the default.

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence alignment. | Readable sequences | Required
-nucmethod | Multiple substitution correction methods for nucleotides. |
0 | (Uncorrected)
1 | (Jukes-Cantor)
2 | (Kimura)
3 | (Tamura)
4 | (Tajima-Nei)
5 | (Jin-Nei Gamma)
| 0
-protmethod | Multiple substitution correction methods for proteins. |
0 | (Uncorrected)
1 | (Jukes-Cantor)
2 | (Kimura Protein)
| 0
[-outf] (Parameter 2) | Enter a name for the distance matrix | Output file | <sequence>.distmat
Optional qualifiers | Allowed values | Default
-ambiguous | Option to use the abiguous codes in the calculation of the Jukes-Cantor method or if the sequences are proteins. | Yes/No | No
-gapweight | Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. | Any integer value | 0.
-position | Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases. | Any integer value | 123
-calculatea | This will force the calculation of the a-parameter in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option). | Yes/No | No
-parametera | User defined a parameter to be use in the Jin-Nei Gamma distance calculation. The suggested value to be used is 1.0 [Jin et al.] and this is the default. | Any integer value | 1.0
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

It reads in a normal multiple sequence alignment file.

The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis.

## Output file format

The output from the program is a file containing a matrix of the calculated distances between each of the input aligned sequences. The distances are expressed in terms of the number of substitutions per 100 bases or amino acids.

The output from the example usage above is:

    Distance Matrix
    ---------------

    Using the Kimura correction method
    Gap weighting is 0.000000

                1       2       3       4       5       6       7       8       9       10
              0.00   96.10  137.41  128.65  161.04  160.26  157.46  154.14  164.22  152.59          PAX4_HUMAN 1
                      0.00  111.86  109.96  156.25  149.70  143.75  135.71  150.60  146.87          PAX6_HUMAN 2
                              0.00   26.21  131.54  143.54  162.95  151.39  163.56  159.78          PAX3_HUMAN 3
                                      0.00  145.45  138.76  158.79  149.96  167.26  161.82          PAX7_HUMAN 4
                                              0.00   44.29  120.84  123.00  131.69  130.22          PAX1_HUMAN 5
                                                      0.00  123.56  130.21  131.64  130.17          PAX9_HUMAN 6
                                                              0.00   36.43   53.12   64.32          PAX2_HUMAN 7
                                                                      0.00   60.88   73.82          PAX5_HUMAN 8
                                                                              0.00   20.37          PX8A_HUMAN 9

## Data files

None.

## Notes

None.

## References

See the following for details of the methods used:

1. "Phylogenetic Inference", Swofford, Olsen, Waddell, and Hillis, in Molecular Systematics, 2nd ed., Sinauer Ass., Inc., 1996, Ch. 11.
2. F. Tajima and M. Nei, Mol. Biol. Evol. 1984, 1, 269.
3. M. Kimura, J. Mol. Evol. 1980, 16, 111.
4. K. Tamura, Mol. Biol. Evol. 1992, 9, 678.
5. L. Jin and M. Nei, Mol. Biol. Evol. 1990, 7, 82.
6. M. Kimura, The Neutral Theory of Molecular Evolution, Camb. Uni. Press, Camb., 1983.

## Warnings

The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---

## Author(s)

This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)

## History

Written (March 2001) - Tim Carver

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments