emix |
Please help by correcting and extending the Wiki pages.
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.