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ednaml |
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5 13 Alpha AACGTGGCCAAAT Beta AAGGTCGCCAAAC Gamma CATTTCGTCACAA Delta GGTATTTCGGCCT Epsilon GGGATCTCGGCCC run with two categories with rates 1.0 and 3.2, and with probabilities 0.4 and 0.6 for these rates, and with patch length parameter = 1.5
% ednaml test -options
Estimates phylogenies from nucleic acid sequence Maximum Likelihood
Output file [ednaml.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 then one category of substitution rates [N]: y
Number of categories of substitution rates [2]:
space seperated categorie values: 1.0 3.2
space seperated probabillity 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
Outgroup root [N]:
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 [ednaml.treefile]:
Nucleic acid sequence Maximum Likelihood method, 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)
+Epsilon
+-------------------------------------------------3
+--2 +----Delta
! !
! +Beta
!
--1---------------------Gamma
!
+---Alpha
remember: this is an unrooted tree!
Ln Likelihood = -72.22209
Examined 15 trees
Between And Length Approx. Confidence Limits
------- --- ------ ------- ---------- ------
1 2 0.06470 ( zero, 0.47007)
2 3 3.33631 ( zero, 12.06173) **
3 Epsilon 0.00003 ( zero, 0.42144)
3 Delta 0.31956 ( zero, 0.73912) **
2 Beta 0.00003 ( zero, 0.41860)
1 Gamma 1.47621 ( zero, 3.63348) **
1 Alpha 0.28041 ( zero, 0.73601) *
* = significantly positive, P < 0.05
** = significantly positive, P < 0.01
Combination of categories that contributes the most to the likelihood:
2222111111 222
% more ednaml.treefile
(((Epsilon:0.00012,Delta:0.31956):3.33631,Beta:0.00012):0.06470,Gamma:1.47621,Alpha:0.28041);
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)
* -outgnum integer number of the outgroup
[-[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 then one category of substitution rates
-og bool Outgroup root
-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 | ednaml.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 |
| -outgnum | number of the outgroup | Integer 1 or more | 1 |
| [-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
| -treefile | Tree file name | Output file | ednaml.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 then one category of substitution rates | Yes/No | No |
| -og | Outgroup root | 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.