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erestml |
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5 13 2 Alpha ++-+-++--+++- Beta ++++--+--+++- Gamma -+--+-++-+-++ Delta ++-+----++--- Epsilon ++++----++---
% erestml test
Restriction site Maximum Likelihood method
Output file [erestml.outfile]: stdout
Randomize input order of species [N]:
Create a tree file [Y]:
Output treefile name [erestml.treefile]:
Restriction site Maximum Likelihood method, version 3.573c
Recognition sequences all 6 bases long
Sites absent from all species are assumed to have been omitted
+Epsilon
+---3
! +Delta
!
! +-----Gamma
--2--1
! +Beta
!
+Alpha
remember: this is an unrooted tree!
Ln Likelihood = -40.35857
Examined 15 trees
Between And Length Approx. Confidence Limits
------- --- ------ ------- ---------- ------
2 3 0.05855 ( 0.05681, 0.06030) **
3 Epsilon 0.00005 ( 0.00000, 0.00010)
3 Delta 0.01458 ( 0.01374, 0.01543) **
2 1 0.00002 ( zero, 0.00006)
1 Gamma 0.11430 ( 0.11177, 0.11683) **
1 Beta 0.00008 ( 0.00002, 0.00014)
2 Alpha 0.02468 ( 0.02357, 0.02578) **
* = significantly positive, P < 0.05
** = significantly positive, P < 0.01
% more erestml.treefile
((Epsilon:0.00005,Delta:0.01458):0.05855,(Gamma:0.11430,
Beta:0.00008):0.00002,Alpha:0.02468);
Mandatory qualifiers (* if not always prompted): [-datafile] infile Input file [-outfile] outfile Output file name * -random bool Randomize input order of species * -randseed integer Random number seed (must be odd) * -randtimes integer How many times to randomise * -outgnum integer number of the outgroup * -datasets integer number of sets [-[no]trout] bool Create a tree file * -treefile outfile Tree file name Optional qualifiers (* if not always prompted): -[no]besttree bool Search for best tree -[no]allsites bool Are all sites detected * -lengths bool Use lengths from user trees -sitelen integer Site length -extrap float Extrapolation factor * -global bool Global rearrangements -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) |
| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-datafile] (Parameter 1) |
Input file | Input file | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | erestml.outfile |
| -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 |
| -outgnum | number of the outgroup | Integer 1 or more | 1 |
| -datasets | number of sets | Integer 2 or more | 2 |
| [-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
| -treefile | Tree file name | Output file | erestml.treefile |
| Optional qualifiers | Allowed values | Default | |
| -[no]besttree | Search for best tree | Yes/No | Yes |
| -[no]allsites | Are all sites detected | Yes/No | Yes |
| -lengths | Use lengths from user trees | Yes/No | No |
| -sitelen | Site length | Integer from 1 to 8 | 6 |
| -extrap | Extrapolation factor | Number 0.001 or more | 100.0 |
| -global | Global rearrangements | 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.