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frestml |
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The assumptions of the present model are:
Note that if the existing base is, say, an A, the chance of it being replaced by a G is 1/3, and so is the chance that it is replaced by a T. This means that there can be no difference in the (expected) rate of transitions and transversions. Users who are upset at this might ponder the fact that a version allowing different rates of transitions and transversions would run an estimated 16 times slower. If it also allowed for unequal frequencies of the four bases, it would run about 300,000 times slower! For the moment, until a better method is available, I guess I'll stick with this one!
Subject to these assumptions, the program is an approximately correct maximum likelihood method.
% frestml Restriction site maximum Likelihood method Input file: restml.dat Phylip tree file (optional): Phylip restml program output file [restml.frestml]: numseqs: 1 Adding species: 1. Alpha 2. Beta 3. Gamma 4. Delta 5. Epsilon Output written to file "restml.frestml" Tree also written onto file "restml.treefile" Done. |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-data] discretestates File containing one or more sets of
restriction data
[-intreefile] tree Phylip tree file (optional)
[-outfile] outfile [*.frestml] Phylip restml program output
file
Additional (Optional) qualifiers (* if not always prompted):
-weights properties Weights file
-njumble integer [0] Number of times to randomise (Integer 0
or more)
* -seed integer [1] Random number seed between 1 and 32767
(must be odd) (Integer from 1 to 32767)
-outgrno integer [0] Species number to use as outgroup
(Integer 0 or more)
-[no]allsites boolean [Y] All sites detected
* -lengths boolean [N] Use lengths from user trees
-sitelength integer [6] Site length (Integer from 1 to 8)
* -global boolean [N] Global rearrangements
* -[no]rough boolean [Y] Speedier but rougher analysis
-[no]trout toggle [Y] Write out trees to tree file
* -outtreefile outfile [*.frestml] Phylip tree output file
-printdata boolean [N] Print data at start of run
-[no]progress boolean [Y] Print indications of progress of run
-[no]treeprint boolean [Y] Print out tree
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory3 string Output directory
"-outtreefile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-data] (Parameter 1) |
File containing one or more sets of restriction data | Discrete states file | |
| [-intreefile] (Parameter 2) |
Phylip tree file (optional) | Phylogenetic tree | |
| [-outfile] (Parameter 3) |
Phylip restml program output file | Output file | <*>.frestml |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -weights | Weights file | Property value(s) | |
| -njumble | Number of times to randomise | Integer 0 or more | 0 |
| -seed | Random number seed between 1 and 32767 (must be odd) | Integer from 1 to 32767 | 1 |
| -outgrno | Species number to use as outgroup | Integer 0 or more | 0 |
| -[no]allsites | All sites detected | Boolean value Yes/No | Yes |
| -lengths | Use lengths from user trees | Boolean value Yes/No | No |
| -sitelength | Site length | Integer from 1 to 8 | 6 |
| -global | Global rearrangements | Boolean value Yes/No | No |
| -[no]rough | Speedier but rougher analysis | Boolean value Yes/No | Yes |
| -[no]trout | Write out trees to tree file | Toggle value Yes/No | Yes |
| -outtreefile | Phylip tree output file | Output file | <*>.frestml |
| -printdata | Print data at start of run | Boolean value Yes/No | No |
| -[no]progress | Print indications of progress of run | Boolean value Yes/No | Yes |
| -[no]treeprint | Print out tree | Boolean value Yes/No | Yes |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
10 35 4
The first line of the data file will also contain a letter W following these numbers (and separated from them by a space) if the Weights option is being used. As with all programs using the weights option, a line or lines must then follow, before the data, with the weights for each site.
The site data are in standard form. Each species starts with a species name whose maximum length is given by the constant "nmlngth" (whose value in the program as distributed is 10 characters). The name should, as usual, be padded out to that length with blanks if necessary. The sites data then follows, one character per site (any blanks will be skipped and ignored). Like the DNA and protein sequence data, the restriction sites data may be either in the "interleaved" form or the "sequential" form. Note that if you are analyzing restriction sites data with the programs DOLLOP or MIX or other discrete character programs, at the moment those programs do not use the "aligned" or "interleaved" data format. Therefore you may want to avoid that format when you have restriction sites data that you will want to feed into those programs.
The presence of a site is indicated by a "+" and the absence by a "-". I have also allowed the use of "1" and "0" as synonyms for "+" and "-", for compatibility with MIX and DOLLOP which do not allow "+" and "-". If the presence of the site is unknown (for example, if the DNA containing it has been deleted so that one does not know whether it would have contained the site) then the state "?" can be used to indicate that the state of this site is unknown.
User-defined trees may follow the data in the usual way. The trees must be unrooted, which means that at their base they must have a trifurcation.
5 13 2 Alpha ++-+-++--+++- Beta ++++--+--+++- Gamma -+--+-++-+-++ Delta ++-+----++--- Epsilon ++++----++--- |
Restriction site Maximum Likelihood method, version 3.68
Recognition sequences all 6 bases long
Sites absent from all species are assumed to have been omitted
+----Gamma
|
| +Beta
1--2
| | +Epsilon
| +--3
| +Delta
|
+Alpha
remember: this is an unrooted tree!
Ln Likelihood = -40.47082
Between And Length Approx. Confidence Limits
------- --- ------ ------- ---------- ------
1 Gamma 0.10794 ( 0.01144, 0.21872) **
1 2 0.01244 ( zero, 0.04712)
2 Beta 0.00100 ( zero, infinity)
2 3 0.05878 ( zero, 0.12675) **
3 Epsilon 0.00022 ( zero, infinity)
3 Delta 0.01451 ( zero, 0.04459) **
1 Alpha 0.01244 ( zero, 0.04717)
* = significantly positive, P < 0.05
** = significantly positive, P < 0.01
|
(Gamma:0.10794,(Beta:0.00100,(Epsilon:0.00022, Delta:0.01451):0.05878):0.01244,Alpha:0.01244); |
| Program name | Description |
|---|---|
| distmat | Create a distance matrix from a multiple sequence alignment |
| ednacomp | DNA compatibility algorithm |
| ednadist | Nucleic acid sequence Distance Matrix program |
| ednainvar | Nucleic acid sequence Invariants method |
| ednaml | Phylogenies from nucleic acid Maximum Likelihood |
| ednamlk | Phylogenies from nucleic acid Maximum Likelihood with clock |
| ednapars | DNA parsimony algorithm |
| ednapenny | Penny algorithm for DNA |
| eprotdist | Protein distance algorithm |
| eprotpars | Protein parsimony algorithm |
| erestml | Restriction site Maximum Likelihood method |
| eseqboot | Bootstrapped sequences algorithm |
| fdiscboot | Bootstrapped discrete sites algorithm |
| fdnacomp | DNA compatibility algorithm |
| fdnadist | Nucleic acid sequence Distance Matrix program |
| fdnainvar | Nucleic acid sequence Invariants method |
| fdnaml | Estimates nucleotide phylogeny by maximum likelihood |
| fdnamlk | Estimates nucleotide phylogeny by maximum likelihood |
| fdnamove | Interactive DNA parsimony |
| fdnapars | DNA parsimony algorithm |
| fdnapenny | Penny algorithm for DNA |
| fdolmove | Interactive Dollo or Polymorphism Parsimony |
| ffreqboot | Bootstrapped genetic frequencies algorithm |
| fproml | Protein phylogeny by maximum likelihood |
| fpromlk | Protein phylogeny by maximum likelihood |
| fprotdist | Protein distance algorithm |
| fprotpars | Protein parsimony algorithm |
| frestboot | Bootstrapped restriction sites algorithm |
| frestdist | Distance matrix from restriction sites or fragments |
| fseqboot | Bootstrapped sequences algorithm |
| fseqbootall | Bootstrapped sequences algorithm |
Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.
Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.