kdnainvar |
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.
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]: |
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) |
4 13 Beta AAGGUCGCCAAAC Gamma CAUUUCGUCACAA Delta GGUAUUUCGGCCU Epsilon GGGAUCUCGGCCC |
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 |
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.
Program name | Description |
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seqret | Reads and writes (returns) sequences |