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epenny |
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7 6
Alpha1 110110
Alpha2 110110
Beta1 110000
Beta2 110000
Gamma1 100110
Delta 001001
Epsilon 001110
% epenny test
Penny algorithm, branch-and-bound to find all most parsimonious trees
Output file [epenny.outfile]: stdout
Method
Wag : Wagner
Cam : Camin-Sokal
Mix : Mixed
prompt : "Choose the method to use
-method : enter list value [Wag]:
Create a tree file [Y]:
Output treefile name [epenny.treefile]:
Wagner parsimony method
requires a total of 8.000
3 trees in all found
+-----------------Alpha1
!
! +--------Alpha2
--1 !
! +-----4 +--Epsilon
! ! ! +--6
! ! +--5 +--Delta
+--2 !
! +-----Gamma1
!
! +--Beta2
+-----------3
+--Beta1
remember: this is an unrooted tree!
+-----------------Alpha1
!
--1 +--------------Alpha2
! !
! ! +--Epsilon
+--2 +--6
! +-----5 +--Delta
! ! !
+--4 +-----Gamma1
!
! +--Beta2
+--------3
+--Beta1
remember: this is an unrooted tree!
+-----------------Alpha1
!
! +-----Alpha2
--1 +--------2
! ! ! +--Beta2
! ! +--3
+--4 +--Beta1
!
! +--Epsilon
! +--6
+--------5 +--Delta
!
+-----Gamma1
remember: this is an unrooted tree!
% more epenny.treefile
(Alpha1,((Alpha2,((Epsilon,Delta),Gamma1)),(Beta2,Beta1)))[0.3333];
(Alpha1,(Alpha2,(((Epsilon,Delta),Gamma1),(Beta2,Beta1))))[0.3333];
(Alpha1,((Alpha2,(Beta2,Beta1)),((Epsilon,Delta),Gamma1)))[0.3333];
Mandatory qualifiers (* if not always prompted): [-infile] infile data file [-outfile] outfile Output file name -method list (no help text) list value * -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: -numgroups integer How many groups of 100 trees -howoften integer How often to report, in trees -simple bool Branch and bound is simple -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 -steps bool Print out steps in each site -seqatnodes bool Print sequences at all nodes of tree -[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 | epenny.outfile | ||||||||
| -method | (no help text) list value |
|
Wag | ||||||||
| -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 3) |
Create a tree file | Yes/No | Yes | ||||||||
| -treefile | Tree file name | Output file | epenny.treefile | ||||||||
| Optional qualifiers | Allowed values | Default | |||||||||
| -numgroups | How many groups of 100 trees | Any integer value | 1000 | ||||||||
| -howoften | How often to report, in trees | Any integer value | 100 | ||||||||
| -simple | Branch and bound is simple | 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 | ||||||||
| -steps | Print out steps in each site | Yes/No | No | ||||||||
| -seqatnodes | Print sequences at all nodes of tree | 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.