gwLee's study

Function

Description

As sequence diverge so does the probability of there being multiplesubstitutions at any one site in the alignment increase. The distancewill then be an underestimate of the true evolutionary distance betweenthe sequences. Therefore, there are a number of methods for correctingthe observed substitution rate for the occurence of multiplesubstutions.

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

Uncorrected distances

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 theflag "-ambiguous" is used then partial matches are included in thescore. 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 zerovalue is given with "-gapweight". It should be noted that end gaps andinternal gaps will be weighted by the same amount. So it is recommendedthat this be used with "-sbegin"and "-send" to specify the start and endof the region to calculate the distance from.

Multiple Substitution correction algorithms

Jukes-Cantor

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 thecalculation of D, by setting the "-ambiguous" and "-gapweight" flags(see "uncorrected distance" method).

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

Tajima-Nei

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

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

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

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 becalculated with an a-value of 1. However, the user can specify their ownvalue, using the "-parametera" option, or calculate for each pair ofsequence, using "-calculatea".

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

Kimura Protein distance

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

% 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 [pax.distmat]: 
 
 

Go to the input files for this example
Go to the output files for this example

Command line arguments

 Standard (Mandatory) qualifiers (* if not always prompted):
 [-sequence] seqset File containing a sequence alignment.
 * -nucmethod menu Multiple substitution correction methods for
 nucleotides.
 * -protmethod menu Multiple substitution correction methods for
 proteins.
 [-outfile] outfile Output file name
 
 Additional (Optional) qualifiers (* if not always prompted):
 * -ambiguous boolean Option to use the ambiguous 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 boolean This will force the calculation of parameter
 'a' in the Jin-Nei Gamma distance
 calculation, otherwise the default is 1.0
 (see -parametera option).
 * -parametera float User defined parameter 'a' 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 (Unprompted) qualifiers: (none)
 Associated qualifiers:
 
 "-sequence" associated qualifiers
 -sbegin1 integer Start of each sequence to be used
 -send1 integer End of each sequence to be used
 -sreverse1 boolean Reverse (if DNA)
 -sask1 boolean Ask for begin/end/reverse
 -snucleotide1 boolean Sequence is nucleotide
 -sprotein1 boolean Sequence is protein
 -slower1 boolean Make lower case
 -supper1 boolean Make upper case
 -sformat1 string Input sequence format
 -sdbname1 string Database name
 -sid1 string Entryname
 -ufo1 string UFO features
 -fformat1 string Features format
 -fopenfile1 string Features file name
 
 "-outfile" associated qualifiers
 -odirectory2 string Output directory
 
 General qualifiers:
 -auto boolean Turn off prompts
 -stdout boolean Write standard output
 -filter boolean Read standard input, write standard output
 -options boolean Prompt for standard and additional values
 -debug boolean Write debug output to program.dbg
 -verbose boolean Report some/full command line options
 -help boolean Report command line options. More
 information on associated and general
 qualifiers can be found with -help -verbose
 -warning boolean Report warnings
 -error boolean Report errors
 -fatal boolean Report fatal errors
 -die boolean Report deaths
 
 
 

Input file format

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

References

1. "Phylogenetic Inference", Swofford, Olsen, Waddell, and Hillis, inMolecular 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.

!!주의할점!!

크리에이티브 커먼즈 라이센스

이 저작물은 크리에이티브 커먼즈 코리아 저작자표시-비영리-변경금지 2.0 대한민국 라이센스에 따라 이용하실 수 있습니다.

Posted by gwlee