|
|
emix |
5 6
Alpha 110110
Beta 110000
Gamma 100110
Delta 001001
Epsilon 001110
% emix test
Mixed parsimony algorithm
Output file [emix.outfile]: stdout
Search for best tree [Y]:
Method
Wag : Wagner
Cam : Camin-Sokal
Mix : Mixed
prompt : "Choose the method to use
-method : enter list value [Wag]:
Outgroup root [N]:
Create a tree file [Y]:
Treefile name [emix.treefile]:
Wagner parsimony method
4 trees in all found
+--Epsilon
+-----4
! +--Gamma
+--2
! ! +--Delta
--1 +-----3
! +--Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
+--------Gamma
!
+--2 +--Epsilon
! ! +--4
! +--3 +--Delta
--1 !
! +-----Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
+--------Epsilon
+--4
! ! +-----Gamma
! +--2
--1 ! +--Delta
! +--3
! +--Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
+--------Gamma
+--2
! ! +-----Epsilon
! +--4
--1 ! +--Delta
! +--3
! +--Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
% more emix.treefile
(((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.2500];
((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.2500];
((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.2500];
((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.2500];
Mandatory qualifiers (* if not always prompted): [-infile] infile data file [-outfile] outfile Output file name [-[no]besttree] bool Search for best tree -method list (no help text) list value * -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 * -valthresh float threshold value * -datasets integer How many data sets [-[no]trout] bool Create a tree file * -treefile outfile Tree file name Optional qualifiers (* if not always prompted): * -random bool Randomize input order of species -ancestral bool Use ancestral states in input file -multsets bool Analyze multiple data sets -printdata bool Print out the data at start of run -progress bool Print indications of progress of run -statesatnodes bool Print states at all nodes of tree -steps bool Print out steps in each character -[no]drawtree bool Draw tree Advanced qualifiers: -thresh bool Use Threshold parsimony |
| Mandatory qualifiers | Allowed values | Default | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| [-infile] (Parameter 1) |
data file | Input file | Required | ||||||||
| [-outfile] (Parameter 2) |
Output file name | Output file | emix.outfile | ||||||||
| [-[no]besttree] (Parameter 3) |
Search for best tree | Yes/No | Yes | ||||||||
| -method | (no help text) list value |
|
Wag | ||||||||
| -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 | ||||||||
| -valthresh | threshold value | Number 1.000 or more | 1.0 | ||||||||
| -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 | emix.treefile | ||||||||
| Optional qualifiers | Allowed values | Default | |||||||||
| -random | Randomize input order of species | Yes/No | No | ||||||||
| -ancestral | Use ancestral states in input file | 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 | ||||||||
| -statesatnodes | Print states at all nodes of tree | Yes/No | No | ||||||||
| -steps | Print out steps in each character | Yes/No | No | ||||||||
| -[no]drawtree | Draw tree | Yes/No | Yes | ||||||||
| Advanced qualifiers | Allowed values | Default | |||||||||
| -thresh | Use Threshold parsimony | Yes/No | No | ||||||||
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.