java -cp path/to/forester.jar org.forester.application.hmmscan_seq_extract
hmmscan_seq_extract [options] <hmmscan output> <fasta file (used as input for hmmscan)> <output dir>
options:
ie: max (inclusive) iE-value
mrel: min (inclusive) relative envelope length ratio
java -Xmx8048m path/to/forester.jar org.forester.application.cladinator3
Usage:
cladinator3 [options] <input tree(s) file> [output table file]
options:
-s=<separator> : the annotation-separator to be used (default: ".")
-m=<mapping table> : to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)
-x : to enable extra processing of annotations (e.g. "Q16611|A.1.1" becomes "A.1.1")
-xs=<separator> : the separator for extra annotations (default: "|")
-xk : to keep extra annotations (e.g. "Q16611|A.1.1" becomes "A.1.1.Q16611")
-S=<pattern> : special processing with pattern (e.g. "(\d+)([a-z]+)_.+" for changing "6q_EF42" to "6.q")
-rs : to remove the annotation-separator in the output (e.g. the ".")
--q=<pattern> : expert option: the regular expression pattern for the query (default: "_#\d+_M=(.+)" for pplacer output)
Examples:
cladinator3 pp_out_tree.sing.tre result.tsv
cladinator3 -s=. pp_out_tree.sing.tre result.tsv
cladinator3 -s=_ -m=map.tsv pp_out_trees.sing.tre result.tsv
cladinator3 -x -xs=& -xk pp_out_trees.sing.tre result.tsv
cladinator3 -x -xs="|" pp_out_trees.sing.tre result.tsv
cladinator3 -x -xk -m=map.tsv pp_out_trees.sing.tre result.tsv
cladinator3 -m=map.tsv -S='(\d+)([a-z?]*)_.+' pp_out_trees.sing.tre result.tsv
Output example:
Input tree : clade_analysis_test_1_2_A.xml
Annotation-separator : .
Query pattern : _#\d+_M=(.+)
Output table : test
Number of input trees : 1
Ext. nodes in input tree : 28
Results:
#Tree # Query Assignment Confidence Brackets Conclusion Placement count
1 Q A.3.1.2 1.0 [A.3.1.2, A.3.1.2] member of clade A.3.1.2 1
java -Xmx2048m -cp path/to/forester.jar org.forester.archaeopteryx.Archaeopteryx
Usage:
Archaeopteryx [-c configuration file] [treefile]