ednapenny |
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Phylip dnapenny documentation.
8 6 Alpha1 AAGAAG Alpha2 AAGAAG Beta1 AAGGGG Beta2 AAGGGG Gamma1 AGGAAG Gamma2 AGGAAG Delta GGAGGA Epsilon GGAAAG
% ednapenny test Penny algorithm for DNA Output file [ednapenny.outfile]: stdout Create a tree file [Y]: Output treefile name [ednapenny.treefile]: Penny algorithm for DNA, version 3.573c branch-and-bound to find all most parsimonious trees requires a total of 8.000 9 trees in all found +--------------------Alpha1 ! ! +--Delta ! +--3 ! +--7 +--Epsilon --1 ! ! ! +-----6 +-----Gamma2 ! ! ! ! +--4 +--------Gamma1 ! ! ! ! ! ! +--Beta2 +--2 +-----------5 ! +--Beta1 ! +-----------------Alpha2 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +-----3 ! ! +--Epsilon --1 +-----6 ! ! ! +--Gamma2 ! ! +-----7 ! +--4 +--Gamma1 ! ! ! ! ! ! +--Beta2 +--2 +-----------5 ! +--Beta1 ! +-----------------Alpha2 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +--3 ! +--6 +--Epsilon --1 ! ! ! +-----7 +-----Gamma1 ! ! ! ! +--4 +--------Gamma2 ! ! ! ! ! ! +--Beta2 +--2 +-----------5 ! +--Beta1 ! +-----------------Alpha2 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +--3 --1 +--7 +--Epsilon ! ! ! ! +--------6 +-----Gamma2 ! ! ! ! ! +--------Gamma1 +--2 ! +--Beta2 ! +--5 +-----------4 +--Beta1 ! +-----Alpha2 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +-----3 --1 ! +--Epsilon ! +--------6 ! ! ! +--Gamma2 ! ! +-----7 +--2 +--Gamma1 ! ! +--Beta2 ! +--5 +-----------4 +--Beta1 ! +-----Alpha2 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +--3 --1 +--6 +--Epsilon ! ! ! ! +--------7 +-----Gamma1 ! ! ! ! ! +--------Gamma2 +--2 ! +--Beta2 ! +--5 +-----------4 +--Beta1 ! +-----Alpha2 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +--3 ! +--7 +--Epsilon --1 ! ! ! +--6 +-----Gamma2 ! ! ! ! +-----2 +--------Gamma1 ! ! ! +--4 +-----------Alpha2 ! ! +--Beta2 +--------------5 +--Beta1 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +-----3 ! ! +--Epsilon --1 +--6 ! ! ! +--Gamma2 ! +-----2 +-----7 ! ! ! +--Gamma1 ! ! ! +--4 +-----------Alpha2 ! ! +--Beta2 +--------------5 +--Beta1 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +--Delta ! +--3 ! +--6 +--Epsilon --1 ! ! ! +--7 +-----Gamma1 ! ! ! ! +-----2 +--------Gamma2 ! ! ! +--4 +-----------Alpha2 ! ! +--Beta2 +--------------5 +--Beta1 remember: this is an unrooted tree! % more ednapenny.treefile (Alpha1,(((((Delta,Epsilon),Gamma2),Gamma1),(Beta2,Beta1)),Alpha2))[0.1111]; (Alpha1,((((Delta,Epsilon),(Gamma2,Gamma1)),(Beta2,Beta1)),Alpha2))[0.1111]; (Alpha1,(((((Delta,Epsilon),Gamma1),Gamma2),(Beta2,Beta1)),Alpha2))[0.1111]; (Alpha1,((((Delta,Epsilon),Gamma2),Gamma1),((Beta2,Beta1),Alpha2)))[0.1111]; (Alpha1,(((Delta,Epsilon),(Gamma2,Gamma1)),((Beta2,Beta1),Alpha2)))[0.1111]; (Alpha1,((((Delta,Epsilon),Gamma1),Gamma2),((Beta2,Beta1),Alpha2)))[0.1111]; (Alpha1,(((((Delta,Epsilon),Gamma2),Gamma1),Alpha2),(Beta2,Beta1)))[0.1111]; (Alpha1,((((Delta,Epsilon),(Gamma2,Gamma1)),Alpha2),(Beta2,Beta1)))[0.1111]; (Alpha1,(((((Delta,Epsilon),Gamma1),Gamma2),Alpha2),(Beta2,Beta1)))[0.1111];
Mandatory qualifiers (* if not always prompted): [-msf] seqset File containing a sequence [-outfile] outfile Output file name * -outgnum integer number of the outgroup * -valthresh float threshold value [-[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 -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 | |
---|---|---|---|
[-msf] (Parameter 1) |
File containing a sequence | Readable sequences | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | ednapenny.outfile |
-outgnum | number of the outgroup | Integer 1 or more | 1 |
-valthresh | threshold value | Number 1.000 or more | 1.0 |
[-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
-treefile | Tree file name | Output file | ednapenny.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 |
-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.