eclique |
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5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110
% eclique test Largest clique program Output file [eclique.outfile]: stdout Create a tree file [Y]: Outgroup root [N]: Largest clique program, version 3.573c Largest Cliques ------- ------- Characters: ( 1 2 3 6) Tree and characters: 2 1 3 6 0 0 1 1 +1-Delta +0--1-+ +--0-+ +--Epsilon ! ! ! +--------Gamma ! +-------------Alpha ! +-------------Beta remember: this is an unrooted tree! % more eclique.treefile (((Delta,Epsilon),Gamma),Alpha,Beta);
Mandatory qualifiers (* if not always prompted): [-infile] infile file to read in [-outfile] outfile Output file name [-[no]trout] bool Create a tree file * -cliqminnum integer Minimum clique size -og bool Outgroup root * -outgnum integer number of the outgroup Optional qualifiers: -[no]drawtree bool Draw tree -ancestral bool Use ancestral states in input file -minclique bool Use minimum clique size -printdata bool Print out the data at start of run -progress bool Print indications of progress of run -matrixout bool Print out compatibility matrix Advanced qualifiers: -treefile outfile tree file name |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-infile] (Parameter 1) |
file to read in | Input file | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | eclique.outfile |
[-[no]trout] (Parameter 3) |
Create a tree file | Yes/No | Yes |
-cliqminnum | Minimum clique size | Any integer value | 1 |
-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 |
-ancestral | Use ancestral states in input file | Yes/No | No |
-minclique | Use minimum clique size | 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 |
-matrixout | Print out compatibility matrix | Yes/No | No |
Advanced qualifiers | Allowed values | Default | |
-treefile | tree file name | Output file | eclique.treefile |
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.