ednamlk |
Please help by correcting and extending the Wiki pages.
% 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.