edolpenny |
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Phylip dolpenny documentation.
7 6 Alpha1 110110 Alpha2 110110 Beta1 110000 Beta2 110000 Gamma1 100110 Delta 001001 Epsilon 001110
% edolpenny test Penny algorithm Dollo or polymorphism Output file [edolpenny.outfile]: stdout Dollo Parsimony method (else Polymorphis) [Y]: Create a tree file [Y]: Output treefile name [edolpenny.treefile]: Penny algorithm for Dollo or polymorphism parsimony, version 3.573c branch-and-bound to find all most parsimonious trees Dollo parsimony method requires a total of 3.000 3 trees in all found +-----------------Delta ! --2 +--------------Epsilon ! ! +--3 +-----------Gamma1 ! ! +--6 +--------Alpha2 ! ! +--1 +--Beta2 ! +--5 +--4 +--Beta1 ! +-----Alpha1 +-----------------Delta ! --2 +--------------Epsilon ! ! +--3 +-----------Gamma1 ! ! +--6 +--Beta2 ! +-----5 ! ! +--Beta1 +--4 ! +--Alpha2 +-----1 +--Alpha1 +-----------------Delta ! --2 +--------------Epsilon ! ! +--3 +-----------Gamma1 ! ! ! ! +--Beta2 +--6 +--5 ! +--4 +--Beta1 ! ! ! +--1 +-----Alpha2 ! +--------Alpha1 % more edolpenny.treefile (Delta,(Epsilon,(Gamma1,(Alpha2,((Beta2,Beta1),Alpha1)))))[0.3333]; (Delta,(Epsilon,(Gamma1,((Beta2,Beta1),(Alpha2,Alpha1)))))[0.3333]; (Delta,(Epsilon,(Gamma1,(((Beta2,Beta1),Alpha2),Alpha1))))[0.3333];
Mandatory qualifiers (* if not always prompted): [-datafile] infile data file [-outfile] outfile Output file name [-[no]dollo] bool Dollo Parsimony method (else Polymorphis) * -valthresh float threshold value * -datasets integer number of 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 -ancest 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 -steps bool Print out steps in each site -statesatnodes bool Print states at all nodes of tree -[no]drawtree bool Draw tree Advanced qualifiers: -thresh bool Use Threshold parsimony |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-datafile] (Parameter 1) |
data file | Input file | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | edolpenny.outfile |
[-[no]dollo] (Parameter 3) |
Dollo Parsimony method (else Polymorphis) | Yes/No | Yes |
-valthresh | threshold value | Number 1.000 or more | 1.0 |
-datasets | number of sets | Integer 2 or more | 2 |
[-[no]trout] (Parameter 4) |
Create a tree file | Yes/No | Yes |
-treefile | Tree file name | Output file | edolpenny.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 |
-ancest | 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 |
-steps | Print out steps in each site | Yes/No | No |
-statesatnodes | Print states 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.