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.