ednainvar |
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Phylip dnainvar documentation.
4 13 Alpha AACGTGGCCAAAT Beta AAGGTCGCCAAAC Gamma CATTTCGTCACAA Delta GGTATTTCGGCCT
% ednainvar test Nucleic acid sequence Invariants method Output file [ednainvar.outfile]: stdout Nucleic acid sequence Invariants method, version 3.573c Pattern Number of times AAAC 1 AAAG 2 AACC 1 AACG 1 CCCG 1 CCTC 1 CGTT 1 GCCT 1 GGGT 1 GGTA 1 TCAT 1 TTTT 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 1 1112 2 1113 3 1121 1 1132 2 1133 1 1231 1 1322 1 1334 1 Tree topologies (unrooted): I: ((Alpha,Beta),(Gamma,Delta)) II: ((Alpha,Gamma),(Beta,Delta)) III: ((Alpha,Delta),(Beta,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 - 0 = 1 0.5000 no II 0 - 0 = 0 1.0000 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 2 8 1 2 Quadratic invariant = 4.0 Chi-square = 0.23111 (not significant) Tree II: Contingency Table 1 5 1 6 Quadratic invariant = -1.0 Chi-square = 0.01407 (not significant) Tree III: Contingency Table 1 2 6 4 Quadratic invariant = 8.0 Chi-square = 0.66032 (not significant) 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: -9.0 Tree II: 4.0 Tree III: 5.0
Mandatory qualifiers: [-msf] seqset File containing sequences [-outfile] outfile Output file name Optional qualifiers: -printdata bool Print out the data at start of run -progress bool Print indications of progress of run Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-msf] (Parameter 1) |
File containing sequences | Readable sequences | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | ednainvar.outfile |
Optional qualifiers | Allowed values | Default | |
-printdata | Print out the data at start of run | Yes/No | No |
-progress | Print indications of progress of run | Yes/No | No |
Advanced qualifiers | Allowed values | Default | |
(none) |
This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.