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efitch |
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5
Alpha 0.000 1.000 2.000 3.000 3.000
Beta 1.000 0.000 2.000 3.000 3.000
Gamma 2.000 2.000 0.000 3.000 3.000
Delta 3.000 3.000 3.000 0.000 1.000
Epsilon 3.000 3.000 3.000 1.000 0.000
% efitch test
Fitch-Margoliash and Least-Squares Distance Methods
Output file [efitch.outfile]: stdout
Search for best tree [Y]:
Outgroup root [N]:
Create a tree file [Y]:
Treefile name [efitch.treefile]:
5 Populations
__ __ 2
\ \ (Obs - Exp)
Sum of squares = /_ /_ ------------
3
i j Obs
Negative branch lengths not allowed
+---------Beta
!
! +---------Epsilon
! +-----------------------------3
--1---------2 +---------Delta
! !
! +-------------------Gamma
!
+---------Alpha
remember: this is an unrooted tree!
Sum of squares = 0.00000
examined 15 trees
Between And Length
------- --- ------
1 Beta 0.50000
1 2 0.50000
2 3 1.50000
3 Epsilon 0.50000
3 Delta 0.50000
2 Gamma 1.00000
1 Alpha 0.50000
% more efitch.treefile
(Beta:0.50000,((Epsilon:0.50000,Delta:0.50000):1.50000,Gamma:1.00000):0.50000,Alpha:0.50000);
Mandatory qualifiers (* if not always prompted): [-infile] infile data file [-outfile] outfile Output file name [-[no]besttree] bool Search for best tree * -randseed integer Random number seed (must be odd) * -randtimes integer Number of times to jumble -og bool Outgroup root * -outgnum integer number of the outgroup * -datasets integer How many data sets [-[no]trout] bool Create a tree file * -treefile outfile Tree file name Optional qualifiers (* if not always prompted): * -length bool Use lengths from user trees -power float Power -negbranch bool Negative branch lengths allowed * -random bool Randomize input order of species * -global bool Global rearrangements -lt bool Lower-triangular data matrix -ut bool Upper-triangular data matrix -replicates bool Subreplicates -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 | |
|---|---|---|---|
| [-infile] (Parameter 1) |
data file | Input file | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | efitch.outfile |
| [-[no]besttree] (Parameter 3) |
Search for best tree | Yes/No | Yes |
| -randseed | Random number seed (must be odd) | Any integer value | 0 |
| -randtimes | Number of times to jumble | Any integer value | 0 |
| -og | Outgroup root | Yes/No | No |
| -outgnum | number of the outgroup | Integer 1 or more | 1 |
| -datasets | How many data sets | Any integer value | 0 |
| [-[no]trout] (Parameter 4) |
Create a tree file | Yes/No | Yes |
| -treefile | Tree file name | Output file | <sequence>.efitch |
| Optional qualifiers | Allowed values | Default | |
| -length | Use lengths from user trees | Yes/No | No |
| -power | Power | Any integer value | 3.0 |
| -negbranch | Negative branch lengths allowed | Yes/No | No |
| -random | Randomize input order of species | Yes/No | No |
| -global | Global rearrangements | Yes/No | No |
| -lt | Lower-triangular data matrix | Yes/No | No |
| -ut | Upper-triangular data matrix | Yes/No | No |
| -replicates | Subreplicates | 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.