kdnainvar

 

Function

Nucleic acid sequence Invariants method using dnainvar

Description

kdnainvar is nucleic acid sequence Invariants method utilizing "dnainvar" methods provided in PHYLIP web service.

Following block is a quotation from fdnainvar included in PHYLIPNEW package. For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants, which test alternative tree topologies. The program also tabulates the frequencies of occurrence of the different nucleotide patterns. Lake's invariants are the method which he calls "evolutionary parsimony". PHYLIP web service is provided by National University of Singapore. Original web-service is located at the following URL:

http://bioportal.bic.nus.edu.sg/phylip/dnainvar.html

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kdnainvaris thus an interface of "runDnainvar" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kdnainvar

% kdnainvar
Nucleic acid sequence Invariants method using dnainvar
Input (gapped) sequence(s): test.fasta
Output file [55-110.kdnainvar]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kdnainvar
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

Input files for usage example

File: sample.dat

     4   13
Beta      AAGGUCGCCAAAC
Gamma     CAUUUCGUCACAA
Delta     GGUAUUUCGGCCU
Epsilon   GGGAUCUCGGCCC

Output file format

Output files for usage example

File: sample.kdnainvar

Nucleic acid sequence Invariants method, version 3.57c



   Pattern   Number of times

     --AA         1
     --AC         1
     AAAA         1
     CCAA         1
     CCCC         2
     GG--         2
     GGGG         1
     GGUC         1
     UCCA         1
     UCUG         1
     UGCA         1
     UUUG         1
     UUUU         1


Symmetrized patterns (1, 2 = the two purines  and  3, 4 = the two pyrimidines
                  or  1, 2 = the two pyrimidines  and  3, 4 = the two purines)

     1111         5
     1113         1
     1133         1
     1134         1
     1213         1
     1223         1
     1324         1

Tree topologies (unrooted): 

    I:  ((Delta,Epsilon),(Gamma,Beta))
   II:  ((Delta,Gamma),(Epsilon,Beta))
  III:  ((Delta,Beta),(Epsilon,Gamma))


Lake's linear invariants
 (these are expected to be zero for the two incorrect tree topologies.
  This is tested by testing the equality of the two parts
  of each expression using a one-sided exact binomial test.
  The null hypothesis is that the first part is no larger than the second.)

 Tree                             Exact test P value    Significant?

   I      1    -     1   =     0       0.7500               no
   II     1    -     0   =     1       0.5000               no
   III    0    -     0   =     0       1.0000               no


Cavender's quadratic invariants (type L) using purines vs. pyrimidines
 (these are expected to be zero, and thus have a nonsignificant
  chi-square, for the correct tree topology)
They will be misled if there are substantially
different evolutionary rate between sites, or
different purine:pyrimidine ratios from 1:1.

  Tree I:

   Contingency Table

      6     2
      0     3

   Quadratic invariant =           -18.0

   Chi-square =    4.95000 (P < 0.05)


  Tree II:

   Contingency Table

      5     2
      0     4

   Quadratic invariant =           -20.0

   Chi-square =    5.23810 (P < 0.05)


  Tree III:

   Contingency Table

      5     0
      2     4

   Quadratic invariant =           -20.0

   Chi-square =    5.23810 (P < 0.05)




Cavender's quadratic invariants (type K) using purines vs. pyrimidines
 (these are expected to be zero for the correct tree topology)
They will be misled if there are substantially
different evolutionary rate between sites, or
different purine:pyrimidine ratios from 1:1.
No statistical test is done on them here.

  Tree I:               0.0
  Tree II:             -2.0
  Tree III:             2.0




Data files

None.

Notes

None.

References


   Felsenstein, J.,(1995) PHYLIP(Phylogeny Interface Package), version3.57c,
      Department of Genetics, University of Washington, Seattle.

   Swofford, D., et al.,(1996) Phylogenetic interface. In Hillis, D.M.,
      Moritz, C., and Mble, B.K.(eds), Molecular Systematics 2nd Edition,
      Sinauer Associates, Mss.


Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org) Institute for Advanced Biosciences, Keio University 252-8520 Japan

History

2009 - Written by Kazuki Oshita

Target users

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

Comments