econsense |
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Phylip consense documentation.
(A,(B,(H,(D,(J,(((G,E),(F,I)),C)))))); (A,(B,(D,((J,H),(((G,E),(F,I)),C))))); (A,(B,(D,(H,(J,(((G,E),(F,I)),C)))))); (A,(B,(E,(G,((F,I),((J,(H,D)),C)))))); (A,(B,(E,(G,((F,I),(((J,H),D),C)))))); (A,(B,(E,((F,I),(G,((J,(H,D)),C)))))); (A,(B,(E,((F,I),(G,(((J,H),D),C)))))); (A,(B,(E,((G,(F,I)),((J,(H,D)),C))))); (A,(B,(E,((G,(F,I)),(((J,H),D),C)))));
% econsense test Majority-rule and strict consensus tree Output file [econsense.outfile]: stdout Create a tree file [Y]: tree file [econsense.treefile]: Majority-rule and strict consensus tree program, version 3.573c Species in order: A B H D J G E F I C Sets included in the consensus tree Set (species in order) How many times out of 9.00 .......**. 9.00 ..******** 9.00 ..***....* 6.00 ..****.*** 6.00 ..***..... 6.00 ..*.*..... 4.00 ..***..*** 2.00 Sets NOT included in consensus tree: Set (species in order) How many times out of 9.00 .....**... 3.00 .....****. 3.00 ..**...... 3.00 .....***** 3.00 ..*.****** 2.00 .....*.**. 2.00 ..****...* 2.00 ....****** 2.00 ...******* 1.00 CONSENSUS TREE: the numbers at the forks indicate the number of times the group consisting of the species which are to the right of that fork occurred among the trees, out of 9.00 trees +---------------------------------------A ! ! +-----------------------------E ! ! ! ! +----I ! ! +------------9.0 ! ! ! +----F ! +--9.0 ! ! ! ! +--2.0 +---------D ! ! ! ! ! +--6.0 ! ! ! ! ! ! ! +----J ! ! ! ! +--6.0 +--4.0 +--9.0 +--6.0 ! +----H ! ! ! ! ! +--------------C ! ! ! +------------------------G ! +----------------------------------B remember: this is an unrooted tree! % more econsense.treefile (A:9.0,((E:9.0,(((I:9.0,F:9.0):9.0,((D:9.0,(J:9.0,H:9.0):4.0):6.0,C:9.0):6.0):2.0,G:9.0):6.0):9.0, B:9.0):9.0);
Mandatory qualifiers (* if not always prompted): [-infile] infile file to read in (New Hampshire standard form) [-outfile] outfile Output file name [-[no]trout] bool Create a tree file [-treefile] outfile tree file name * -og bool Outgroup root * -outgnum integer number of the outgroup Optional qualifiers: -[no]drawtree bool Draw tree -root bool Trees to be treated as Rooted -progress bool Print indications of progress of run -[no]printsets bool Print out the sets of species Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-infile] (Parameter 1) |
file to read in (New Hampshire standard form) | Input file | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | econsense.outfile |
[-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
[-treefile] (Parameter 4) |
tree file name | Output file | econsense.treefile |
-og | Outgroup root | Yes/No | No |
-outgnum | number of the outgroup | Integer 1 or more | 1 |
Optional qualifiers | Allowed values | Default | |
-[no]drawtree | Draw tree | Yes/No | Yes |
-root | Trees to be treated as Rooted | Yes/No | No |
-progress | Print indications of progress of run | Yes/No | No |
-[no]printsets | Print out the sets of species | Yes/No | Yes |
Advanced qualifiers | Allowed values | Default | |
(none) |
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.