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econtml |
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5 10 2 2 2 2 2 2 2 2 2 2 European 0.2868 0.5684 0.4422 0.4286 0.3828 0.7285 0.6386 0.0205 0.8055 0.5043 African 0.1356 0.4840 0.0602 0.0397 0.5977 0.9675 0.9511 0.0600 0.7582 0.6207 Chinese 0.1628 0.5958 0.7298 1.0000 0.3811 0.7986 0.7782 0.0726 0.7482 0.7334 American 0.0144 0.6990 0.3280 0.7421 0.6606 0.8603 0.7924 0.0000 0.8086 0.8636 Australian 0.1211 0.2274 0.5821 1.0000 0.2018 0.9000 0.9837 0.0396 0.9097 0.2976
% econtml test Continuous character Maximum Likelihood method Output file [econtml.outfile]: stdout Global rearrangements [N]: Randomize input order of species [N]: Input file has all alleles at each locus [N]: Create a tree file [Y]: Output treefile name [econtml.treefile]: 5 Populations, 10 Loci +----------------------------------African ! ! +--------American --1--------------2 ! ! +-----------------------Australian ! +--------------------3 ! +Chinese ! +--European remember: this is an unrooted tree! Ln Likelihood = 33.29060 examined 15 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 1 African 0.08464 ( 0.02351, 0.17917) 1 2 0.03569 ( -0.00262, 0.09493) 2 American 0.02094 ( -0.00904, 0.06731) 2 3 0.05098 ( 0.00555, 0.12124) 3 Australian 0.05959 ( 0.01775, 0.12430) 3 Chinese 0.00221 ( -0.02034, 0.03710) 1 European 0.00624 ( -0.01948, 0.04601) % more econtml.treefile (African:0.08464,(American:0.02094,(Australian:0.05959,Chinese:0.00221):0.05098):0.03569, European:0.00624);
Mandatory qualifiers (* if not always prompted):
[-infile] infile input file
[-outfile] outfile Output file name
* -lengths bool Use lengths from user trees
* -global bool Global rearrangements
* -random bool Randomize input order of species
* -randseed integer Random number seed (must be odd)
* -all bool Input file has all alleles at each locus
* -outgnum integer number of the outgroup
* -datasets integer How many data sets
[-[no]trout] bool Create a tree file
* -treefile outfile Tree file name
Optional qualifiers:
-[no]besttree bool Search for best tree
-continuous bool continuous characters (else Gene
frequencies)
-og bool Outgroup root
-multsets bool Analyze multiple data sets
-printdata bool Print out the data at start of run
-progress bool Print indications of progress of run
-[no]drawtree bool Draw tree
Advanced qualifiers: (none)
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-infile] (Parameter 1) |
input file | Input file | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | econtml.outfile |
| -lengths | Use lengths from user trees | Yes/No | No |
| -global | Global rearrangements | Yes/No | No |
| -random | Randomize input order of species | Yes/No | No |
| -randseed | Random number seed (must be odd) | Any integer value | 3 |
| -all | Input file has all alleles at each locus | Yes/No | No |
| -outgnum | number of the outgroup | Integer 1 or more | 1 |
| -datasets | How many data sets | Integer 1 or more | 1 |
| [-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
| -treefile | Tree file name | Output file | econtml.treefile |
| Optional qualifiers | Allowed values | Default | |
| -[no]besttree | Search for best tree | Yes/No | Yes |
| -continuous | continuous characters (else Gene frequencies) | Yes/No | No |
| -og | Outgroup root | Yes/No | No |
| -multsets | Analyze multiple data sets | Yes/No | No |
| -printdata | Print out the data at start of run | Yes/No | No |
| -progress | Print indications of progress of run | Yes/No | No |
| -[no]drawtree | Draw tree | Yes/No | Yes |
| 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.