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ednamlk |
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% ednamlk test -options
Estimates phylogenies from nucleic acid sequence Maximum Likelihood with
molecular clock
Output file [ednamlk.outfile]: stdout
Search for best tree [Y]:
Global rearrangements [N]:
Randomize input order of species [N]:
Transition/transversion ratio [2.0]:
Use empirical base frequencies [Y]:
More than one category of substitution rates [N]: y
Number of categories of substitution rates [2]:
space seperated category values: 1.0 3.2
space seperated probabilliyy values: 0.4 0.6
Use Defualt Mean block length of sites [N]:
Mean block length of sites having the same rate (greater than 1) [1.0]: 1.5
Print out the data at start of run [N]:
Print indications of progress of run [N]:
Draw tree [Y]:
Create a tree file [Y]:
Output treefile name [ednamlk.treefile]:
Nucleic acid sequence
Maximum Likelihood method with molecular clock, version 3.573c
Site category Rate of change Probability
1 1.000 0.400
2 3.200 0.600
Expected length of a patch of sites having the same rate = 1.500
Empirical Base Frequencies:
A 0.24615
C 0.29231
G 0.24615
T(U) 0.21538
Transition/transversion ratio = 2.000000
(Transition/transversion parameter = 1.523077)
+--Delta
+--------------------------------------------------------4
! +--Epsilon
--3
! +-------------Gamma
+---------------------------------------------2
! +--Alpha
+----------1
+--Beta
Ln Likelihood = -72.40499
Ancestor Node Node Time Length
-------- ---- ---- ---- ------
root 3
3 4 3.40036 3.40036
4 Delta 3.55871 0.15834
4 Epsilon 3.55871 0.15834
3 2 2.75249 2.75249
2 Gamma 3.55871 0.80621
2 1 3.38652 0.63403
1 Alpha 3.55871 0.17218
1 Beta 3.55871 0.17218
Combination of categories that contributes the most to the likelihood:
2222221111 112
% more ednamlk.treefile
((Delta:0.15834,Epsilon:0.15834):3.40036,(Gamma:0.80621,
(Alpha:0.17218,Beta:0.17218):0.63403):2.75249);
Mandatory qualifiers (* if not always prompted):
[-msf] seqset File containing a sequence allignment
[-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)
* -randtimes integer How many times to randomise
* -freqa float Frequency for A
* -freqc float Frequency for C
* -freqg float Frequency for G
* -freqt float Frequency for T/U
* -catnum integer Number of categories of substitution rates
* -catvals string space seperated category values
* -catprob string space seperated probabillity values
* -autog bool Use Defualt Mean block length of sites
* -lambda float Mean block length of sites having the same
rate (greater than 1)
[-[no]trout] bool Create a tree file
* -treefile outfile Tree file name
Optional qualifiers:
-[no]besttree bool Search for best tree
-ttratio float Transition/transversion ratio
-[no]basefrequency bool Use empirical base frequencies
-categories bool More than one category of substitution rates
-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)
|
| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-msf] (Parameter 1) |
File containing a sequence allignment | Readable sequences | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | ednamlk.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 |
| -randtimes | How many times to randomise | Any integer value | 3 |
| -freqa | Frequency for A | Number from 0.000 to 1.000 | 0.25 |
| -freqc | Frequency for C | Number from 0.000 to 1.000 | 0.25 |
| -freqg | Frequency for G | Number from 0.000 to 1.000 | 0.25 |
| -freqt | Frequency for T/U | Number from 0.000 to 1.000 | 0.25 |
| -catnum | Number of categories of substitution rates | Integer from 2 to 9 | 2 |
| -catvals | space seperated category values | Any string is accepted | An empty string is accepted |
| -catprob | space seperated probabillity values | Any string is accepted | An empty string is accepted |
| -autog | Use Defualt Mean block length of sites | Yes/No | No |
| -lambda | Mean block length of sites having the same rate (greater than 1) | Number 1.000 or more | 1.0 |
| [-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
| -treefile | Tree file name | Output file | ednamlk.treefile |
| Optional qualifiers | Allowed values | Default | |
| -[no]besttree | Search for best tree | Yes/No | Yes |
| -ttratio | Transition/transversion ratio | Any integer value | 2.0 |
| -[no]basefrequency | Use empirical base frequencies | Yes/No | Yes |
| -categories | More than one category of substitution rates | 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.